Enzymatic Nucleic Acid Synthesis

ABSTRACT

The disclosure provides methods for making a polynucleotide wherein the addition of nucleotides can be physically, chemically and/or enzymatically controlled. The methods include combining a selected nucleotide, cations, an error prone or template independent DNA polymerase at a reaction site including an initiator sequence attached thereto and having a 3′ terminal nucleotide, wherein the reaction reagents can be modulated and under conditions that allow covalent addition of one or more of a selected nucleotide to the 3′ terminal nucleotide such that the selected nucleotide becomes a 3′ terminal nucleotide, and repeating the addition step until the polynucleotide is formed.

RELATED APPLICATION DATA

This application is a National Stage Application under 35 U.S.C. 371 ofco-pending PCT application PCT/US17/24939 designating the United Statesand filed Mar. 30, 2017; which claims the benefit of U.S. ProvisionalApplication No. 62/317,919 filed on Apr. 4, 2016 which is herebyincorporated herein by reference in its entirety for all purposes.

STATEMENT OF GOVERNMENT INTERESTS

This invention was made with government support under MH103910 awardedby the National Institutes of Health. The government has certain rightsin the invention.

SEQUENCE LISTING

The instant application contains a Sequence Listing which has beensubmitted electronically in ASCII format and is hereby incorporated byreference in its entirety. Said ASCII copy, created on Oct. 2, 2018, isnamed 19381040_1.txt and is 2,661 bytes in size.

FIELD

The present invention relates in general to methods of makingoligonucleotides and polynucleotides using enzymatic synthesis.

BACKGROUND

DNA has been proposed as a highly desirable medium for storage ofdigital information. The barrier to such use of DNA is the lowefficiency and speed as well as the high cost of current synthesismethods. In the current state of the art, DNA is synthesized usingphosphoramidite precursors in organic solvents. These chemical synthesismethods result in errors of approximately 1% and take approximately 10minutes per addition step. Furthermore, the reagents that are used inthis synthesis process are expensive. Some of these same reagents alsodamage DNA, a problem that precludes the possibility of synthesizing DNAstrands that are longer than ˜200 bases, further hampering theefficiency of this chemical process. Despite multiple efforts, afeasible method for synthesis of custom nucleic acid sequences usingterminal deoxynucleotidyl transferase (TdT) has not been describedbefore. TdT is currently used in batch reactions for the addition ofvariable lengths of singular nucleotides or uncontrolled sequence ofnucleotide mixtures to the 3′ end of a nucleic acid sequence. A methodto control the number and nature of nucleotides that TdT incorporates togenerate user-defined nucleic acid sequences is a significant challengewhich has not been addressed. There thus remains a need for thedevelopment of faster and cheaper enzymatic oligonucleotide synthesismethods than the existing chemical oligonucleotide synthesis methods.

SUMMARY

The present disclosure addresses this need and is based on the discoveryof methods that synthesize nucleic acids of a desired sequence using atemplate-independent DNA polymerase. The methods according to thedisclosure sequentially expose nucleic acid polymers to nucleotidepolymerization units (NPUs) that extend the polymer by an expectedlength. The disclosure provides that each NPU comprises terminaldeoxynucleotidyl transferase (TdT) and one type of nucleotide substrate(such as A, C, G, and T/U). The nucleotide substrates are in the form ofnucleotide triphosphates which are the active form for polymerizationpurposes as contemplated by the present disclosure. The disclosureprovides novel physical, chemical, and enzymatic methods to control NPUextensions and limit them to a few nucleotides. These novel methodsovercome problems encountered under commonly used laboratory conditionsin which NPUs would extend nucleic acid polymers indefinitely anduncontrollably. These novel methods provide sequential exposure of theDNA polymers to NPUs that contain different nucleotides and obtainnucleic acid polymers of a desired sequence, thus serving a basis forenzymatic encoding of digital information into DNA. These novel methodsprovide improved control of the number and nature of nucleotides thattemplate-independent DNA polymerases, such as TdT, incorporate intonucleic acid polymers and enable user-defined synthesis of nucleic acidsequences useful for biological applications.

The most relevant enzyme for do novo synthesis of nucleic acidsaccording to the disclosure is terminal deoxynucleotidyl transferase(TdT), a unique DNA polymerase which extends single-strandedoligonucleotides. Critically, TdT is template-independent, a propertythat enables the incorporation of bases into a growing strand of nucleicacids based on availability of provided nucleotides. This property makesTdT an attractive DNA polymerase for de novo DNA synthesis.

The disclosure provides that under ideal circumstances, it is desirableto limit the number of additions by TdT to one. Such DNA is not onlysuitable for digital information storage but also for use inbiological/genetic application. The disclosure further provides thatlimiting the additions to one is not necessarily required for storage ofinformation into DNA. An exemplary proper encoding strategy that,instead of considering each base as a unit of information, considerseach stretch of one or more identical bases (i.e., a homopolymer) as aunit of information can be used for digital storage purposes. Forinstance, if every stretch of A or T represents 0 and every stretch of Cor G represents 1, the sequence “AAATTAACCCCGGACTTAAGGGCC” (SEQ IDNO: 1) would be equivalent to “ATACGACTAGC” (SEQ ID NO: 2) and wouldrepresent “00011010011”.

The present disclosure provides a method for making a polynucleotidecomprising (a) delivering a reaction reagent mobile phase including atleast an error prone template independent DNA polymerase, a selectednucleotide triphosphate and cations along a fluidic channel to areaction site, wherein the reaction site includes an initiator attachedthereto and having a 3′ terminal nucleotide, wherein reaction reagentsare present in the reaction reagent mobile phase at selectedconcentrations, wherein the reaction reagent mobile phase has a selectedvolume and a selected flow rate to achieve a selected residence time atthe reaction site under conditions which covalently add one or more ofthe selected nucleotide to the 3′ terminal nucleotide such that theselected nucleotide becomes a 3′ terminal nucleotide, (b) delivering anorganic wash mobile phase to the reaction site at a fluid flow rate toremove the reaction reagents from the reaction site, and (c) repeatingsteps (a) and (b) until the polynucleotide is formed, with the provisothat step (b) is not required to be performed after the polynucleotideis formed.

The present disclosure provides a method for making a polynucleotidecomprising (a) combining a selected nucleotide triphosphate, cations, anerror prone or template independent DNA polymerase, and a nucleotidetriphosphate inactivating enzyme at a reaction site including aninitiator sequence attached thereto and having a 3′ terminal nucleotide,wherein reaction reagents are present at selected concentrations andunder conditions which covalently add one or more of the selectednucleotide to the 3′ terminal nucleotide such that the selectednucleotide becomes a 3′ terminal nucleotide and under conditions whichinactivate free nucleotide triphosphates until free nucleotidetriphosphates are substantially inactivated, wherein a desired number ofthe selected nucleotide is added to the initiator sequence, and (b)repeating step (a) until the polynucleotide is formed.

The present disclosure provides a method for making a polynucleotidecomprising (a) combining a selected inactive nucleotide, cations, anerror prone or template independent DNA polymerase at a reaction siteincluding an initiator sequence attached thereto and having a 3′terminal nucleotide, activating the selected inactive nucleotide,wherein reaction reagents are present at selected concentrations andunder conditions which covalently add one or more of a selectedactivated nucleotide to the 3′ terminal nucleotide such that theselected activated nucleotide becomes a 3′ terminal nucleotide and underconditions wherein a desired number of the selected activated nucleotideis added to the initiator sequence, and (b) repeating step (a) until thepolynucleotide is formed.

The present disclosure also provides a method for making apolynucleotide comprising (a) combining a selected nucleotidetriphosphate, cations, an inactive error prone or template independentDNA polymerase at a reaction site including an initiator sequenceattached thereto and having a 3′ terminal nucleotide, activating theinactive error prone or template independent DNA polymerase, whereinreaction reagents are present at selected concentrations and underconditions which covalently add one or more of a selected nucleotide tothe 3′ terminal nucleotide such that the selected nucleotide becomes a3′ terminal nucleotide and under conditions wherein a desired number ofthe selected nucleotide is added to the initiator sequence, and (b)repeating step (a) until the polynucleotide is formed.

The present disclosure provides a method for making a polynucleotidecomprising (a) combining a selected nucleotide triphosphate, cations, anerror prone or template independent DNA polymerase at a reaction siteincluding an initiator sequence attached thereto and having a 3′terminal nucleotide, wherein reaction reagents are present at selectedconcentrations and under conditions which covalently add one or more ofa selected nucleotide to the 3′ terminal nucleotide such that theselected nucleotide becomes a 3′ terminal nucleotide and wherein theerror prone or template independent DNA polymerase is inactivated toterminate addition of the selected nucleotide, and (b) repeating step(a) until the polynucleotide is formed.

The present disclosure further provides a method for making apolynucleotide comprising (a) combining a selected inactive nucleotide,cations, an inactive error prone or template independent DNA polymeraseat a reaction site including an initiator sequence attached thereto andhaving a 3′ terminal nucleotide, activating the nucleotide andactivating the error prone or template independent DNA polymerase,wherein reaction reagents are present at selected concentrations andunder conditions which covalently add one or more of a selectednucleotide to the 3′ terminal nucleotide such that the selectednucleotide becomes a 3′ terminal nucleotide, and (b) repeating step (a)until the polynucleotide is formed.

Further features and advantages of certain embodiments of the presentinvention will become more fully apparent in the following descriptionof embodiments and drawings thereof, and from the claims.

BRIEF DESCRIPTION OF THE DRAWINGS

The patent or application file contains at least one drawing executed incolor. Copies of this patent or patent application publication withcolor drawing(s) will be provided by the Office upon request and paymentof the necessary fee. The foregoing and other features and advantages ofthe present embodiments will be more fully understood from the followingdetailed description of illustrative embodiments taken in conjunctionwith the accompanying drawings in which:

FIGS. 1A & 1B depict in schematic a physical control method of NPUexposure to nucleic acid polymers in a fluidic device. FIG. 1A depictsin schematic a top-down view of sequence of NPUs as they flow over theinitiator oligo patch. FIG. 1B depicts in schematic a microfluidicdevice which implements this physical control.

FIGS. 2A & 2B depict in schematic a chemical control method of NPUexposure to nucleic acid polymers in a fluidic device. FIG. 2A depictsin schematic NPU in a solution with TdT and apyrase covering aninitiator oligo. FIG. 2B depicts in schematic polymerization that occurswhen each base is deposited onto the NPU.

FIG. 3 depicts screened nucleotide analog substrates for TdT to selectfor better performance on extension efficiency, rate, and extensionlength distribution according to the embodiments of the disclosedmethods.

FIG. 4 depicts in schematic an apparatus which implements certainembodiments of the disclosed methods for TdT-based NPU synthesis of DNAwith given information content. Initiator DNA is immobilized to a glasssurface and the desired nucleotide is deposited on the DNA. NPUsincluding TdT and apyrase are deposited to catalyze a limited extension.After cleanup, the oligo is ready for the deposition of the nextnucleotide and NPUs.

FIG. 5 depicts in schematic a PDMS mask template for generating amicrofluidic device which implements the physical control of NPUexposure to nucleic acid polymers.

FIG. 6 depicts PCR products on Agarose gel according to the embodimentsof the disclosed methods.

FIG. 7 depicts quantification of the number of nucleotides added to theoligonucleotide initiator for each nucleotide type and concentration inaddition to the number of oligonucleotide initiators that receivednonzero addition of nucleotides for each nucleotide type andconcentration according to the embodiments of the disclosed methods andas measured by high-throughput single-molecule sequencing.

FIG. 8 depicts fraction of initiators with nonzero addition ofnucleotides per nucleotide concentration according to the embodiments ofthe disclosed methods.

FIG. 9 depicts 3′-modified reversible terminators.

FIG. 10 depicts 3′-modified reversible terminators.

FIG. 11 depicts base-modified nucleotides.

FIG. 12 depicts a schematic of the divalent cations that changepolymerization mechanism and thereby efficiency and kinetics ofpolymerization.

FIG. 13 depicts results for pH regulation of TdT enzyme activity on aTBE-Urea gel according to the embodiments of the disclosed methods.

FIG. 14 depicts results for reversible pH regulation of TdT enzymeactivity on a TBE-Urea gel according to the embodiments of the disclosedmethods.

FIG. 15 is a gel image showing results for 5BR-dCTP and 5I-dCTP.

FIG. 16 is a gel image showing results for 5h-dCTP and 5hm-dCTP.

FIG. 17 is a gel image showing results for 5m-dCTP and dCTP.

DETAILED DESCRIPTION

The present disclosure provides methods of modulating activity ofcomponents and reagents used in template independent nucleic acidsynthesis, such as nucleotides, template independent polymerase, andcations. The residence time of each of these components at a reactionsite can be altered to modulate addition of a nucleotide to an initiatorsequence or a growing nucleic acid chain. Each of these components canbe activated or deactivated to modulate the addition of a nucleotide toan initiator sequence or growing nucleic acid chain. In this manner,nucleotide addition can be controlled to a desired number ofnucleotides, such as one nucleotide, two nucleotides, three nucleotidesetc. The disclosure provides that addition is limited to one nucleotide,two nucleotides, three nucleotides or more during one round ofnucleotide addition. This activation or inactivation of the reactioncomponents may be reversible to allow for multiple rounds of nucleotidepolymerization that each adds a different nucleotide to the primer orgrowing polynucleotide chain.

The present disclosure provides methods of “mobile-phase oligonucleotidesynthesis,” an enzymatic synthesis that enables control over the numberand nature of nucleotides that an error prone or template independentpolymerase such as TdT adds to a primer strand of DNA, i.e., theprimer/initiator for DNA synthesis. According to certain aspects of thepresent disclosure, the methods involve a fluidic/microfluidic devicewherein initiator oligonucleotides (nucleic acids that act as theinitial substrate for TdT to extend with the desired sequence) areimmobilized on the surface of this device in a patch (i.e., theinitiator patch). The patch is then exposed to “packets” of reagentsthat include TdT pre-mixed with one of the four possible nucleotidetriphosphates (dNTPs). In some embodiments, the microfluidic deviceaccurately controls the exact exposure time of the patch to eachTdT-dNTP packet, thus limiting the addition to a desired count or adesired distribution of counts. In certain embodiment, the device alsoallows control over the order of packets, thereby enabling control overthe incorporated sequence. For instance, for the synthesis of thesequence “GATC,” the patch will be exposed to a packet of TdT-dGTP,followed by a packet of TdT-dATP, followed by a packet of TdT-TTP,followed by a packet of TdT-dCTP wherein the patch is exposed to eachpacket for an optimal time that ensures single additions or additions ofa desired length or length distribution by the enzyme.

The disclosure provides a variety of ways to achieve precise controlover the number of nucleotides that are added by TdT. In one embodiment,the disclosure provides “kinetic” control wherein each packet residesover the patch for a period of time long enough for a single additionbut too short for two or more additions. In another embodiment, thedisclosure provides combining the kinetic control with various chemicaland biochemical approaches to achieve control over the number ofadditions of nucleotides that are added by TdT. In certain exemplaryembodiments, instead of natural dNTPs, reversible terminator dNTPs canbe used. Terminator dNTPs are modified dNTPs that TdT can add to agrowing DNA primer but cannot extend further. In such a system, aftereach reversible terminator dNTP-TdT packet, a packet that reverts thetermination chemically, physically, or enzymatically will also beintroduced, followed by the next desired reversible terminator dNTP-TdTpacket, and so on. In yet another embodiment, controlling the number ofadditions is achieved by using an engineered TdT or packet compositionwherein the TdT enzyme remains bound to the primer at some stage in itscatalytic cycle, thus blocking further additions. The next packet canallow the enzyme to complete the catalytic cycle and detach but lack anydNTPs so unwanted additions can be prevented.

The present disclosure provides that an important property of themobile-phase synthesis strategy is that more than one liquid phase canbe used in the microfluidic device. In certain embodiments, an inertorganic phase, such as mineral oil, can be used to separate TdT-dNTPpackets to make sure that their contents do not mix and the initiatorpatch is cleaned of residual content from the previous TdT-dNTP packet.An organic phase between the packets also ensures a sharp packet borderand thus achieves very precise control over the exposure time of thepatch to each packet. In some embodiments, the use of active chemicalsin this organic phase that for instance reverse termination byterminator nucleotides is also contemplated.

The present disclosure provides that another important property of themobile-phase synthesis strategy is that it allows a different conditionto be used in each of the four TdT-dNTP packet types. This is importantas the kinetics of the enzyme may be different for different dNTPs.Thus, to obtain optimal results, different conditions, such as type andconcentration of divalent ions may need to be used for different dNTPs.

The present disclosure provides methods of the mobile-phaseoligonucleotide synthesis which enable rapid and high-accuracy synthesisof custom DNA sequences by the template-independent DNA-polymeraseterminal deoxynucleotidyl transferase (TdT). The methods according tothe present disclosure can be used for synthesis of cheaper, moreaccurate and longer custom DNA sequences for various biochemical,biomedical, or biosynthetic applications. Furthermore, given thepotential for high-speed DNA synthesis, the methods according to thepresent disclosure can facilitate the use of DNA as an informationstorage medium. In this case, a solid-phase synthesis device can be usedto record digital information in DNA molecules.

Embodiments of the disclosure are directed to a method for making apolynucleotide wherein addition of the nucleotides can be physicallycontrolled. In one embodiment, the method comprises (a) delivering areaction reagent mobile phase including at least an error prone templateindependent DNA polymerase, a selected nucleotide triphosphate andcations along a fluidic channel to a reaction site, wherein the reactionsite includes an initiator attached thereto and having a 3′ terminalnucleotide, wherein reaction reagents are present in the reactionreagent mobile phase at selected concentrations, wherein the reactionreagent mobile phase has a selected volume and a selected flow rate toachieve a selected residence time at the reaction site under conditionswhich covalently add one or more of the selected nucleotide to the 3′terminal nucleotide such that the selected nucleotide becomes a 3′terminal nucleotide, (b) delivering an organic wash mobile phase to thereaction site at a fluid flow rate to remove the reaction reagents fromthe reaction site, and (c) repeating steps (a) and (b) until thepolynucleotide is formed, with the proviso that step (b) is not requiredto be performed after the polynucleotide is formed.

In one embodiment, the selected volume and selected flow rate for thereaction reagent mobile phase is determined based on reactivity of theselected nucleotide triphosphate present in the reaction reagent mobilephase. In another embodiment, the selected volume and selected flow ratefor the reaction reagent mobile phase differ based on the selectednucleotide triphosphate present in the reaction reagent mobile phase. Incertain embodiment, the selected flow rate for the reaction reagentmobile phase is constant and the selected volume differs based on theselected nucleotide triphosphate present in the reaction reagent mobilephase. In one embodiment, the selected volume of the reaction reagentmobile phase is constant and the selected flow rate differs based on theselected nucleotide triphosphate present in the reaction reagent mobilephase. In another embodiment, the selected flow rate for the reactionreagent mobile phase is constant and the selected volume differs basedon the selected nucleotide triphosphate present in the reaction reagentmobile phase and the desired number of the selected nucleotides to beadded to the 3′ end of the polynucleotide. In another embodiment, theselected volume of the reaction reagent mobile phase is constant and theselected flow rate differs based on the selected nucleotide triphosphatepresent in the reaction reagent mobile phase and the desired number ofthe selected nucleotides to be added to the 3′ end of thepolynucleotide.

In one embodiment, the reaction site is a surface area on the surface ofthe fluidic channel. In another embodiment, the selected concentrationof reaction reagents in the reaction reagent mobile phase is determinedby the selected nucleotide triphosphate present in the reaction reagentmobile phase. In another embodiment, the reaction site is within thefluidic channel. In one embodiment, the reaction site is a structurewithin the fluidic channel. In one embodiment, the reaction site is acollection of beads within the fluidic channel. In one embodiment, thereaction site is an electrode on the surface of the fluidic channel. Inanother embodiment, the reaction site is an electrode within the fluidicchannel. In one embodiment, the initiator includes one or morenucleotides. In one embodiment, the residence time is sufficient tolimit the number of covalent additions of the selected nucleotide.

In some embodiments, the organic wash mobile phase is immiscible withthe reaction reagent mobile phase. In one embodiment, the reactionreagent mobile phase is bounded on either end by an organic wash mobilephase. In another embodiment, the organic wash mobile phase inactivatesthe reaction reagent mobile phase at the reaction site. In a certainembodiment, an air plug is used instead of or in addition to the organicwash mobile phase. In one embodiment, an aqueous wash mobile phase isused instead of or in addition to the organic wash mobile phase. Inanother embodiment, an aqueous wash mobile phase is used instead of orin addition to an air plug. In yet another embodiment, a plurality ofreaction reagent mobile phases bounded on either end by an organic washmobile phase flow to the reaction site.

The method according to the present disclosure further includes the stepof monitoring covalent addition of the selected nucleotide. In oneembodiment, the error prone template independent DNA polymerase isterminal deoxynucleotide transferase. In another embodiment, the cationsare one or more of Zn⁺², Co⁺², Mg⁺² or Mn⁺².

The method according to the disclosure provides that the selectednucleotide is a natural nucleotide or a nucleotide analog. In someembodiments, the selected nucleotide is a member selected from the groupconsisting of

In one embodiment, the reaction reagent mobile phase includes a buffercomprising a monovalent salt, a divalent salt, a buffering agent, and areducing agent at a suitable pH and temperature. In another embodiment,the reaction reagent mobile phase includes a buffer comprising 10 to 20mM tris-acetate, 20 to 50 mM potassium acetate, 5 to 8 mM magnesiumacetate, 0.5 to 1.0 mM DTT and with a pH of about 2 to 12 and at atemperature of about 10 and 80° C. In one embodiment, the reactionreagent mobile phase includes a buffer comprising 14 mM tris-acetate, 35mM potassium acetate, 7 mM magnesium acetate, 0.7 mM DTT and with a pHof about 7.9 and at a temperature of about 25° C.

Certain embodiment of the disclosure is directed to an initiator that isattached by a cleavable moiety.

The method according to the disclosure further comprises releasing thepolynucleotide from the reaction site after the desired sequence ofnucleotides has been added to the 3′ end of the polynucleotide. Themethod according to the disclosure further comprises releasing thepolynucleotide from the reaction site using an enzyme, a chemical,light, heat or other suitable method or reagent. The method according tothe disclosure further comprises releasing the polynucleotide from thereaction site, collecting the polynucleotide, amplifying thepolynucleotide and sequencing the polynucleotide.

Embodiments of the disclosure are directed to a method for making apolynucleotide wherein the addition of nucleotides can be chemicallycontrolled via inactivating active nucleotide triphosphates using anenzyme. In one embodiment, the method comprises (a) combining a selectednucleotide triphosphate, cations, an error prone or template independentDNA polymerase, and a nucleotide triphosphate inactivating enzyme at areaction site including an initiator sequence attached thereto andhaving a 3′ terminal nucleotide, wherein reaction reagents are presentat selected concentrations and under conditions which covalently add oneor more of the selected nucleotide to the 3′ terminal nucleotide suchthat the selected nucleotide becomes a 3′ terminal nucleotide and underconditions which inactivate free nucleotide triphosphates until freenucleotide triphosphates are substantially inactivated, wherein adesired number of the selected nucleotide is added to the initiatorsequence, and (b) repeating step (a) until the polynucleotide is formed.

In one embodiment, the nucleotide inactivating enzyme is a nucleotidetriphosphate degrading enzyme. In one embodiment, the nucleotidetriphosphate inactivating enzyme is a nucleotide triphosphate degradingenzyme that degrades nucleotide triphosphates at a rate slower than rateof addition of nucleotides by the error prone or template independentDNA polymerase.

In certain embodiment, the nucleotide triphosphate inactivating enzymeis a nucleotide triphosphate degrading enzyme present at a concentrationthat degrades nucleotide triphosphates at a rate slower than rate ofaddition of nucleotides by the present concentration of the error proneor template independent DNA polymerase. In some embodiments, thenucleotide triphosphate inactivating enzyme comprises ATPdiphosphohydrolase, dNTP pyrophosphatases, dNTPases, and phosphatases.

In one embodiment, the concentration of nucleotide triphosphateinactivating enzyme is modulated to control addition of one or morenucleotides. In one embodiment, the nucleotide triphosphate inactivatingenzyme renders free nucleotide triphosphates inactive. In oneembodiment, the nucleotide inactivating enzyme renders free nucleotidetriphosphates inactive by degradation. In another embodiment, thenucleotide inactivating enzyme renders free nucleotide triphosphatesinactive by polymerizing them with each other. In certain embodiment,the reaction conditions present a competing reaction between addition offree nucleotide triphosphates to the initiator sequence and degradationof free nucleotide triphosphates.

In one embodiment, the selected nucleotide is added to the reaction siteincluding the initiator sequence having the terminal nucleotide, theerror prone or template independent DNA polymerase and the nucleotideinactivating enzyme. In another embodiment, the error prone or templateindependent DNA polymerase and the nucleotide inactivating enzyme areadded to the reaction site including the initiator sequence having theterminal nucleotide, and the selected nucleotide. In certain embodiment,the nucleotide inactivating enzyme is added to the reaction siteincluding the initiator sequence having the terminal nucleotide, theerror prone or template independent DNA polymerase and the selectednucleotide under conditions where the polymerase is inactive, andwherein the polymerase is activated upon addition of the nucleotideinactivating enzyme. In some embodiments, step (b) is repeated aplurality of times after which the reaction reagents are removed fromthe reaction site and additional reaction reagents are provided to thereaction site. In one embodiment, the reaction reagents are removed fromthe reaction site and additional reaction reagents are provided to thereaction site after each round of addition. In another embodiment, thereaction reagents are removed from the reaction site and additionalreaction reagents are provided to the reaction site after each round ofaddition.

Embodiments of the disclosure are directed to a method for making apolynucleotide wherein the addition of nucleotides can be chemicallycontrolled via activating inactive nucleotides. In one embodiment, themethod comprises (a) combining a selected inactive nucleotide, cations,an error prone or template independent DNA polymerase at a reaction siteincluding an initiator sequence attached thereto and having a 3′terminal nucleotide, activating the selected inactive nucleotide,wherein reaction reagents are present at selected concentrations andunder conditions which covalently add one or more of a selectedactivated nucleotide to the 3′ terminal nucleotide such that theselected activated nucleotide becomes a 3′ terminal nucleotide and underconditions wherein a desired number of the selected activated nucleotideis added to the initiator sequence, and (b) repeating step (a) until thepolynucleotide is formed.

In one embodiment, the inactive nucleotide is rendered active by achemical reaction, an enzyme, heat, light or pH. In another embodiment,the inactive nucleotide includes a protecting group and the protectinggroup is removed. In some embodiments, the inactive nucleotide comprisesNPE or DMNPE-caged nucleotides or similar caged nucleotides that areactivated by light, heat, an enzyme, a chemical reaction, or pH. In acertain embodiment, the NPE-caged nucleotides comprise deoxynucleotide5′-Triphosphate, P3-(1-(2-Nitrophenyl)Ethyl) esters. In a certainembodiment, the DMNPE-caged nucleotides comprise deoxynucleotide5′-Triphosphate, P3-(1-(4,5-Dimethoxy-2-Nitrophenyl)ethyl) esters.

In one embodiment, the selected inactive nucleotide is a nucleoside,nucleotide monophosphate, or nucleotide diphosphate form that isrendered into the active nucleotide triphosphate form by an activatingenzyme such as nucleotide diphosphate kinase. In another embodiment, theinactive nucleotide is rendered active at a rate which allows additionof one or more activated nucleotides. In one embodiment, the inactivenucleotide is rendered active at a rate which allows addition of one ormore activated nucleotides after which either the activated nucleotidesor the polymerase is rendered inactive. In another embodiment, theinactive nucleotide is rendered active allowing addition of one or moreactivated nucleotides after which the polymerase is rendered inactive.In yet another embodiment, the polymerase is rendered inactive by achemical reaction, divalent cations, an enzyme, heat, light or pH.

In one embodiment, the selected inactive nucleotide is added to thereaction site including the initiator sequence having the terminalnucleotide, and the error prone or template independent DNA polymeraseand the inactive nucleotide is activated. In some embodiments, step (b)is repeated a plurality of times after which the reaction reagents areremoved from the reaction site and additional reaction reagents areprovided to the reaction site.

Embodiments of the disclosure are directed to a method for making apolynucleotide wherein the addition of nucleotides can be chemically andenzymatically controlled via activating an inactive polymerase. In oneembodiment, the method comprises (a) combining a selected nucleotidetriphosphate, cations, an inactive error prone or template independentDNA polymerase at a reaction site including an initiator sequenceattached thereto and having a 3′ terminal nucleotide, activating theinactive error prone or template independent DNA polymerase, whereinreaction reagents are present at selected concentrations and underconditions which covalently add one or more of a selected nucleotide tothe 3′ terminal nucleotide such that the selected nucleotide becomes a3′ terminal nucleotide and under conditions wherein a desired number ofthe selected nucleotide is added to the initiator sequence, and (b)repeating step (a) until the polynucleotide is formed.

In one embodiment, the inactive error prone or template independent DNApolymerase is rendered active by a chemical reaction, divalent cations,an enzyme, heat, light or pH. In some embodiments, the inactive errorprone or template independent DNA polymerase is rendered active by achemical reaction, an enzyme, heat, light or pH and rendered inactiveagain by a chemical reaction, an enzyme, heat, light or pH afteraddition of the desired number of the selected nucleotide onto theinitiator. In one embodiment, the inactive error prone or templateindependent DNA polymerase includes a protecting group and theprotecting group is removed. In certain embodiment, the protecting groupcomprises a chemical group that is incorporated into the polymerase andis removable by light, heat, pH, or enzymes to control the polymeraseactivity.

In one embodiment, the inactive error prone or template independent DNApolymerase is rendered active at a rate which allows addition of one ormore nucleotides. In another embodiment, the inactive error prone ortemplate independent DNA polymerase is rendered active at a rate whichallows addition of one or more nucleotides after which either thenucleotides or the polymerase is rendered inactive. In one embodiment,the inactive error prone or template independent DNA polymerase isrendered active allowing addition of one or more nucleotides after whichthe polymerase is rendered inactive. In one embodiment, the polymeraseis rendered inactive by a chemical reaction, an enzyme, heat, light orpH. In certain embodiment, the inactive error prone or templateindependent DNA polymerase is added to the reaction site including theinitiator sequence having the terminal nucleotide, and the selectednucleotide triphosphate and wherein the inactive error prone or templateindependent DNA polymerase is activated. In some embodiments, step (b)is repeated a plurality of times after which the reaction reagents areremoved from the reaction site and additional reaction reagents areprovided to the reaction site.

Embodiments of the disclosure are directed to a method for making apolynucleotide wherein the addition of nucleotides can be chemically andenzymatically controlled via inactivating active polymerase. In oneembodiment, the method comprises (a) combining a selected nucleotidetriphosphate, cations, an error prone or template independent DNApolymerase at a reaction site including an initiator sequence attachedthereto and having a 3′ terminal nucleotide, wherein reaction reagentsare present at selected concentrations and under conditions whichcovalently add one or more of a selected nucleotide to the 3′ terminalnucleotide such that the selected nucleotide becomes a 3′ terminalnucleotide and wherein the error prone or template independent DNApolymerase is inactivated to terminate addition of the selectednucleotide, and (b) repeating step (a) until the polynucleotide isformed.

In one embodiment, the inactive error prone or template independent DNApolymerase is rendered active by a chemical reaction, an enzyme, heat,light or pH. In another embodiment, the active error prone or templateindependent DNA polymerase is rendered inactive by a chemical reaction,an enzyme, heat, light or pH after the addition of a desired number ofthe selected nucleotide and rendered active again by a chemicalreaction, an enzyme, heat, light or pH for the addition of the nextselected nucleotide to the 3′ terminal nucleotide of the polynucleotide.In one embodiment, the inactive error prone or template independent DNApolymerase includes a protecting group and the protecting group isremoved. In certain embodiments, the protecting group comprises achemical group that is incorporated into the polymerase and is removableby light, heat, pH, or enzymes to control the polymerase activity.

In one embodiment, the error prone or template independent DNApolymerase is rendered inactive at a rate which allows addition of oneor more nucleotides. In another embodiment, the error prone or templateindependent DNA polymerase is rendered inactive at a rate which allowsaddition of one or more nucleotides. In yet another embodiment, theerror prone or template independent DNA polymerase is added to thereaction site including the initiator sequence having the terminalnucleotide, and the selected nucleotide triphosphate and wherein theerror prone or template independent DNA polymerase is rendered inactive.In some embodiments, step (b) is repeated a plurality of times afterwhich the reaction reagents are removed from the reaction site andadditional reaction reagents are provided to the reaction site.

Embodiments of the disclosure are directed to a method for making apolynucleotide wherein the addition of nucleotides can be chemically andenzymatically controlled via activating the nucleotide and thepolymerase. In one embodiment, the method comprises (a) combining aselected inactive nucleotide, cations, an inactive error prone ortemplate independent DNA polymerase at a reaction site including aninitiator sequence attached thereto and having a 3′ terminal nucleotide,activating the nucleotide and activating the error prone or templateindependent DNA polymerase, wherein reaction reagents are present atselected concentrations and under conditions which covalently add one ormore of a selected nucleotide to the 3′ terminal nucleotide such thatthe selected nucleotide becomes a 3′ terminal nucleotide, and (b)repeating step (a) until the polynucleotide is formed.

In one embodiment, either the active nucleotide or the active errorprone or template independent DNA polymerase is rendered inactive toterminate addition of the selected nucleotide. In another embodiment,the active error prone or template independent DNA polymerase isrendered inactive by a chemical reaction, an enzyme, heat, light or pHafter the addition of a desired number of the selected nucleotide andrendered active again by a chemical reaction, an enzyme, heat, light orpH for the addition of the next selected nucleotide to the 3′ terminalnucleotide of the polynucleotide. In one embodiment, the inactive errorprone or template independent DNA polymerase is rendered active by achemical reaction, an enzyme, heat, light or pH. In another embodiment,the inactive error prone or template independent DNA polymerase includesa protecting group and the protecting group is removed. In someembodiments, the protecting group comprises a chemical group that isincorporated into the polymerase and is removable by light, heat, pH, orenzymes to control the polymerase activity. In one embodiment, theinactive nucleotide is rendered active by a chemical reaction, anenzyme, heat, light or pH. In another embodiment, the inactivenucleotide includes a protecting group and the protecting group isremoved. In some embodiments, the inactive nucleotide comprisesNPE-caged nucleotides or similar caged nucleotides that are removed bylight, heat, an enzyme, a chemical reaction, or pH. In certainembodiment, the NPE-caged nucleotides comprise deoxynucleotide5′-Triphosphate, P3-(1-(2-Nitrophenyl)Ethyl) esters. In someembodiments, the selected inactive nucleotide in a nucleoside,nucleotide monophosphate, or nucleotide diphosphate form that isrendered into the active nucleotide triphosphate form by an activatingenzyme such as nucleotide diphosphate kinase. In certain embodiment,either the inactive nucleotide or inactive error prone or templateindependent DNA polymerase is rendered active at a rate which allowsaddition of one or more nucleotides. In some embodiments, step (b) isrepeated a plurality of times after which the reaction reagents areremoved from the reaction site and additional reaction reagents areprovided to the reaction site.

Polymerases, including without limitation error-prone ortemplate-dependent polymerases, modified or otherwise, can be used tocreate nucleotide polymers having a random or known or desired sequenceof nucleotides. Template-independent polymerases, whether modified orotherwise, can be used to create the nucleic acids de novo. Ordinarynucleotides are used, such as A, T/U, C or G. Nucleotides may be usedwhich lack chain terminating moieties. Reversible terminators may beused in the methods of making the nucleotide polymers. A templateindependent polymerase may be used to make the nucleic acid sequence.Such template independent polymerase may be error-prone which may leadto the addition of more than one nucleotide resulting in a homopolymer.

Oligonucleotide sequences or polynucleotide sequences are synthesizedusing an error prone polymerase, such as template independent errorprone polymerase, and common or natural nucleic acids, which may beunmodified. Initiator sequences or primers are attached to a substrate,such as a silicon dioxide substrate, at various locations whether known,such as in an addressable array, or random. Reagents including at leasta selected nucleotide, a template independent polymerase and otherreagents required for enzymatic activity of the polymerase are appliedat one or more locations of the substrate where the initiator sequencesare located and under conditions where the polymerase adds one or morethan one or a plurality of the nucleotide to the initiator sequence toextend the initiator sequence. The nucleotides (“dNTPs”) may be appliedor flow in periodic applications. Nucleotides with blocking groups orreversible terminators can be used with the dNTPs under reactionconditions that are sufficient to limit or reduce the probability ofenzymatic addition of the dNTP to one dNTP, i.e. one dNTP is added usingthe selected reaction conditions taking into consideration the reactionkinetics. Nucleotides with blocking groups or reversible terminators areknown to those of skill in the art. According to an additionalembodiment when reaction conditions permit, more than one dNTP may beadded to form a homopolymer run when common or natural nucleotides areused with a template independent error prone polymerase.

Polymerase activity may be modified using protease, photo-chemical orelectrochemical modulation as a reaction condition so as to minimizeaddition of dNTP beyond a single dNTP. A wash is then applied to the oneor more locations to remove the reagents. The steps of applying thereagents and the wash are repeated until desired nucleic acids arecreated. According to one aspect, the reagents may be added to one ormore than one or a plurality of locations on the substrate in series orin parallel or the reagents may contact the entire surface of thesupport, such as by flowing the reagents across the surface of thesupport. According to one aspect, the reaction conditions aredetermined, for example based on reaction kinetics or the activity ofthe polymerase, so as to limit the ability of the polymerase to attachmore than one nucleotide to the end of the initiator sequence or thegrowing oligonucleotide.

In addition, according to certain embodiments, polymerases can bemodulated to be light sensitive for light based methods. According tothis aspect, light is modulated to tune the polymerase to add only asingle nucleotide. The light is shone on individual locations or pixelsof the substrate where the polymerase, the nucleotide and appropriatereagents and reaction conditions are present. In this manner, anucleotide is added to an initiator sequence or an existing nucleotideas the polymerase is activated by the light. In certain embodiments,polymerase activity can be controlled by pH. It is well known to askilled in the art that each polymerase has an active pH range outsideof which it is inactive. In one embodiment, the reaction reagent pH canadjusted in and out of the active range to control the polymerase. In anexemplary embodiment, it has been determined that TdT is active below pH10 but is inactive at pH 11. Therefore, if the initial setup of thereaction is at pH 11, temporarily changing the pH to anywhere below 10can temporarily activate the TdT enzyme. Furthermore, divalent cationssuch as Mg++, Co++, Mn++, Zn++, Ni++, are also known to a skilled inthat art to be necessary for the activity of all known DNA polymerases.Chelating divalent cations from the reaction can stop the polymerase, orreleasing divalent cations into the reaction can activate thepolymerase. Engineered polymerases can be created which are made activeby a certain wavelength of light and made inactive by another wavelengthof light. Such polymerases can contain light-reactive groups such asAzobenzene, Spiropyran, or Retinal. Engineered polymerases can be madethat are rendered inactive at a certain temperature but are reactivatedat another. Natural polymerases are also known to have this quality butto a limited and less useful level as compared to engineeredpolymerases. Additionally, there exists a competitive, non-competitive,or uncompetitive chemical inhibitor of the polymerase such as Acyclovir(Zovirax) which and can be “caged” by light, pH, or heat such that itcan be reversibly released/absorbed or activated/inactivated to controlthe activity of the polymerase.

A flow cell or other channel, such a microfluidic channel ormicrofluidic channels having an input and an output is used to delivermobile phase or reaction fluids including reagents, such as apolymerase, a nucleotide and other appropriate reagents and washes toparticular locations on a substrate within the flow cell, such as withina microfluidic channel. One of skill will recognize that reactionconditions will be based on dimensions of the substrate reaction region,reagents, concentrations, reaction temperature, and the structures usedto create and deliver the reagents and washes. According to certainaspects, pH and other reactants and reaction conditions can be optimizedfor the use of TdT to add a dNTP to an existing nucleotide oroligonucleotide in a template independent manner. For example, Ashley etal., Virology 77, 367-375 (1977) hereby incorporated by reference in itsentirety identifies certain reagents and reaction conditions for dNTPaddition, such as initiator size, divalent cation and pH. TdT wasreported to be active over a wide pH range with an optimal pH of 6.85.Methods of providing or delivering dNTP, rNTP or rNDP are useful inmaking nucleic acids. Release of a lipase or other membrane-lytic enzymefrom pH-sensitive viral particles inside dNTP filled-liposomes isdescribed in J Clin Microbiol. May 1988; 26(5): 804-807. Photo-cagedrNTPs or dNTPs from which NTPs can be released, typically nitrobenzylderivatives sensitive to 350 nm light, are commercially available fromLife Technologies. Rhoposin or bacterio-opsin triggered signaltransduction resulting in vesicular or other secretion of nucleotides isknown in the art. With these methods for delivering dNTPs, thenucleotides should be removed or sequestered between the firstprimer-polymerase encountered and any downstream.

Terms and symbols of nucleic acid chemistry, biochemistry, genetics, andmolecular biology used herein follow those of standard treatises andtexts in the field, e.g., Kornberg and Baker, DNA Replication, SecondEdition (W.H. Freeman, New York, 1992); Lehninger, Biochemistry, SecondEdition (Worth Publishers, New York, 1975); Strachan and Read, HumanMolecular Genetics, Second Edition (Wiley-Liss, New York, 1999);Eckstein, editor, Oligonucleotides and Analogs: A Practical Approach(Oxford University Press, New York, 1991); Gait, editor, OligonucleotideSynthesis: A Practical Approach (IRL Press, Oxford, 1984); and the like.

Nucleic Acids and Nucleotides

As used herein, the terms “nucleic acid molecule,” “nucleic acidsequence,” “nucleic acid fragment” and “oligomer” are usedinterchangeably and are intended to include, but are not limited to, apolymeric form of nucleotides that may have various lengths, includingeither deoxyribonucleotides or ribonucleotides, or analogs thereof.

In general, the terms “nucleic acid molecule,” “nucleic acid sequence,”“nucleic acid fragment,” “oligonucleotide” and “polynucleotide” are usedinterchangeably and are intended to include, but not limited to, apolymeric form of nucleotides that may have various lengths, eitherdeoxyribonucleotides (DNA) or ribonucleotides (RNA), or analogs thereof.A oligonucleotide is typically composed of a specific sequence of fournucleotide bases: adenine (A); cytosine (C); guanine (G); and thymine(T) (uracil (U) for thymine (T) when the polynucleotide is RNA).According to certain aspects, deoxynucleotides (dNTPs, such as dATP,dCTP, dGTP, dTTP) may be used. According to certain aspects,ribonucleotide triphosphates (rNTPs) may be used. According to certainaspects, ribonucleotide diphosphates (rNDPs) may be used.

The term “oligonucleotide sequence” is the alphabetical representationof a polynucleotide molecule; alternatively, the term may be applied tothe polynucleotide molecule itself. This alphabetical representation canbe input into databases in a computer having a central processing unitand used for bioinformatics applications such as functional genomics andhomology searching. Oligonucleotides may optionally include one or morenon-standard nucleotide(s), nucleotide analog(s) and/or modifiednucleotides. The present disclosure contemplates any deoxyribonucleotideor ribonucleotide and chemical variants thereof, such as methylated,hydroxymethylated or glycosylated forms of the bases, and the like.According to certain aspects, natural nucleotides are used in themethods of making the nucleic acids. Natural nucleotides lack chainterminating moieties.

Examples of modified nucleotides include, but are not limited todiaminopurine, S2T, 5-fluorouracil, 5-bromouracil, 5-chlorouracil,5-iodouracil, hypoxanthine, xantine, 4-acetylcytosine,5-(carboxyhydroxylmethyl)uracil,5-carboxymethylaminomethyl-2-thiouridine,5-carboxymethylaminomethyluracil, dihydrouracil,beta-D-galactosylqueosine, inosine, N6-isopentenyladenine,1-methylguanine, 1-methylinosine, 2,2-dimethylguanine, 2-methyladenine,2-methylguanine, 3-methylcytosine, 5-methylcytosine, N6-adenine,7-methylguanine, 5-methylaminomethyluracil,5-methoxyaminomethyl-2-thiouracil, beta-D-mannosylqueosine,5′-methoxycarboxymethyluracil, 5-methoxyuracil,2-methylthio-D46-isopentenyladenine, uracil-5-oxyacetic acid (v),wybutoxosine, pseudouracil, queosine, 2-thiocytosine,5-methyl-2-thiouracil, 2-thiouracil, 4-thiouracil, 5-methyluracil,uracil-5-oxyacetic acid methylester, uracil-5-oxyacetic acid (v),5-methyl-2-thiouracil, 3-(3-amino-3-N-2-carboxypropyl) uracil, (acp3)w,2,6-diaminopurine and the like. Nucleic acid molecules may also bemodified at the base moiety (e.g., at one or more atoms that typicallyare available to form a hydrogen bond with a complementary nucleotideand/or at one or more atoms that are not typically capable of forming ahydrogen bond with a complementary nucleotide), sugar moiety orphosphate backbone. Nucleic acid molecules may also containamine-modified groups, such as aminoallyl-dUTP (aa-dUTP) andaminohexhylacrylamide-dCTP (aha-dCTP) to allow covalent attachment ofamine reactive moieties, such as N-hydroxy succinimide esters (NHS).

Alternatives to standard DNA base pairs or RNA base pairs in theoligonucleotides of the present disclosure can provide higher density inbits per cubic mm, higher safety (resistant to accidental or purposefulsynthesis of natural toxins), easier discrimination in photo-programmedpolymerases, or lower secondary structure. Such alternative base pairscompatible with natural and mutant polymerases for de novo and/oramplification synthesis are described in Betz K, Malyshev D A, LavergneT, Welte W, Diederichs K, Dwyer T J, Ordoukhanian P, Romesberg F E, MarxA (2012) KlenTaq polymerase replicates unnatural base pairs by inducinga Watson-Crick geometry, Nature Chem. Biol. 8:612-614; See Y J, MalyshevD A, Lavergne T, Ordoukhanian P, Romesberg F E. J Am Chem Soc. 2011 Dec.14; 133(49):19878-88, Site-specific labeling of DNA and RNA using anefficiently replicated and transcribed class of unnatural base pairs;Switzer C Y, Moroney S E, Benner S A. (1993) Biochemistry.32(39):10489-96. Enzymatic recognition of the base pair betweenisocytidine and isoguanosine; Yamashige R, Kimoto M, Takezawa Y, Sato A,Mitsui T, Yokoyama S, Hirao I. Nucleic Acids Res. 2012 March;40(6):2793-806. Highly specific unnatural base pair systems as a thirdbase pair for PCR amplification; and Yang Z, Chen F, Alvarado J B,Benner S A. J Am Chem Soc. 2011 Sep. 28; 133(38):15105-12,Amplification, mutation, and sequencing of a six-letter syntheticgenetic system. Other non-standard nucleotides may be used such asdescribed in Malyshev, D. A., et al., Nature, vol. 509, pp. 385-388 (15May 2014) hereby incorporated by reference in its entirety.

Polymerases

According to an alternate embodiment of the present invention,polymerases are used to build nucleic acid molecules, such as forrepresenting information which is referred to herein as being recordedin the nucleic acid sequence or the nucleic acid is referred to hereinas being storage media. Polymerases are enzymes that produce a nucleicacid sequence, for example, using DNA or RNA as a template. Polymerasesthat produce RNA polymers are known as RNA polymerases, whilepolymerases that produce DNA polymers are known as DNA polymerases.Polymerases that incorporate errors are known in the art and arereferred to herein as an “error-prone polymerases”. Template independentpolymerases may be error prone polymerases. Using an error-pronepolymerase allows the incorporation of specific bases at preciselocations of the DNA molecule. Error-prone polymerases will eitheraccept a non-standard base, such as a reversible chain terminating base,or will incorporate a different nucleotide, such as a natural orunmodified nucleotide that is selectively given to it as it tries tocopy a template. Template-independent polymerases such as terminaldeoxynucleotidyl transferase (TdT), also known as DNAnucleotidylexotransferase (DNTT) or terminal transferase create nucleicacid strands by catalyzing the addition of nucleotides to the 3′terminus of a DNA molecule without a template. The preferred substrateof TdT is a 3′-overhang, but it can also add nucleotides to blunt orrecessed 3′ ends. Cobalt is a cofactor, however the enzyme catalyzesreaction upon Mg and Mn administration in vitro. Nucleic acid initiatorsmay be 4 or 5 nucleotides or longer and may be single stranded or doublestranded. Double stranded initiators may have a 3′ overhang or they maybe blunt ended or they may have a 3′ recessed end.

TdT, like all DNA polymerases, also requires divalent metal ions forcatalysis. However, TdT is unique in its ability to use a variety ofdivalent cations such as Co2+, Mn2+, Zn2+ and Mg2+. In general, theextension rate of the primer p(dA)n (where n is the chain length from 4through 50) (SEQ ID NO: 3) with dATP in the presence of divalent metalions is ranked in the following order: Mg2+>Zn2+>Co2+>Mn2+. In addition,each metal ion has different effects on the kinetics of nucleotideincorporation. For example, Mg2+ facilitates the preferentialutilization of dGTP and dATP whereas Co2+ increases the catalyticpolymerization efficiency of the pyrimidines, dCTP and dTTP. Zn2+behaves as a unique positive effector for TdT since reaction rates withMg2+ are stimulated by the addition of micromolar quantities of Zn2+.This enhancement may reflect the ability of Zn2+ to induceconformational changes in TdT that yields higher catalytic efficiencies.Polymerization rates are lower in the presence of Mn2+ compared to Mg2+,suggesting that Mn2+ does not support the reaction as efficiently asMg2+. Further description of TdT is provided in Biochim Biophys Acta.,May 2010; 1804(5): 1151-1166 hereby incorporated by reference in itsentirety. In addition, one may replace Mg2+, Zn2+, Co2+, or Mn2+ in thenucleotide pulse with other cations designed modulate nucleotideattachment. For example, if the nucleotide pulse replaces Mg++ withother cation(s), such as Na+, K+, Rb+, Be++, Ca++, or Sr++, then thenucleotide can bind but not incorporate, thereby regulating whether thenucleotide will incorporate or not. Then a pulse of (optional) pre-washwithout nucleotide or Mg++ can be provided or then Mg++ buffer withoutnucleotide can be provided.

By controlling the primer/initiator, the nucleotide substrate, or thepolymerase, the incorporation of specific nucleic acids into the polymercan be regulated. Thus, these polymerases are capable of incorporatingnucleotides independent of the template sequence and are thereforebeneficial for creating nucleic acid sequences de novo. The combinationof an error-prone polymerase and a primer sequence serves as a writingmechanism for imparting information into a nucleic acid sequence.

By controlling the primer/initiator, the nucleotide substrate, or thetemplate independent polymerase, the addition of a nucleotide to aninitiator sequence or an existing nucleotide or oligonucleotide can beregulated to produce an oligonucleotide by extension. Thus, thesepolymerases are capable of incorporating nucleotides without a templatesequence and are therefore beneficial for creating nucleic acidsequences de novo.

The eta-polymerase (Matsuda et al. (2000) Nature 404(6781):1011-1013) isan example of a polymerase having a high mutation rate (˜10%) and hightolerance for 3′ mismatch in the presence of all 4 dNTPs and probablyeven higher if limited to one or two dNTPs. Hence, the eta-polymerase isa de novo recorder of nucleic acid information similar to terminaldeoxynucleotidyl transferase (TdT) but with the advantage that theproduct produced by this polymerase is continuously double-stranded.Double stranded DNA has less sticky secondary structure and has a morepredictable secondary structure than single stranded DNA. Furthermore,double stranded DNA serves as a good support for polymerases and/orDNA-binding-protein tethers.

According to certain aspects, a template dependent or templatesemi-dependent error prone polymerase can be used. According to certainembodiments, a template dependent polymerase may be used which maybecome error prone. According to certain embodiments, a templateindependent RNA polymerase can be used. Where a template dependent ortemplate semi-dependent polymerase is used, any combination of templateswith universal bases can be used which encourage acceptance of manynucleotide types. In addition, error tolerant cations such as Mn⁺ can beused. Further, the present disclosure contemplates the use oferror-tolerant polymerase mutants. See Berger et al., Universal Basesfor Hybridization, Replication and Chain Termination, Nucleic AcidsResearch 2000, Aug. 1, 28(15) pp. 2911-2914 hereby incorporated byreference. Methods of activating or inactivating template independentpolymerases known to those of skill in the art are useful in the presentdisclosure.

Supports and Attachment

In certain exemplary embodiments, one or more oligonucleotide sequencesdescribed herein are immobilized on a support (e.g., a solid and/orsemi-solid support). In certain aspects, an oligonucleotide sequence canbe attached to a support using one or more of the phosphoramiditelinkers described herein. Suitable supports include, but are not limitedto, slides, beads, chips, particles, strands, gels, sheets, tubing,spheres, containers, capillaries, pads, slices, films, plates and thelike. In various embodiments, a solid support may be biological,nonbiological, organic, inorganic, or any combination thereof. Supportsof the present invention can be any shape, size, or geometry as desired.For example, the support may be square, rectangular, round, flat,planar, circular, tubular, spherical, and the like. When using a supportthat is substantially planar, the support may be physically separatedinto regions, for example, with trenches, grooves, wells, or chemicalbarriers (e.g., hydrophobic coatings, etc.). Supports may be made fromglass (silicon dioxide), metal, ceramic, polymer or other materialsknown to those of skill in the art. Supports may be a solid, semi-solid,elastomer or gel. In certain exemplary embodiments, a support is amicroarray. As used herein, the term “microarray” refers in oneembodiment to a type of array that comprises a solid phase supporthaving a substantially planar surface on which there is an array ofspatially defined non-overlapping regions or sites that each contain animmobilized hybridization probe. “Substantially planar” means thatfeatures or objects of interest, such as probe sites, on a surface mayoccupy a volume that extends above or below a surface and whosedimensions are small relative to the dimensions of the surface. Forexample, beads disposed on the face of a fiber optic bundle create asubstantially planar surface of probe sites, or oligonucleotidesdisposed or synthesized on a porous planar substrate create asubstantially planar surface. Spatially defined sites may additionallybe “addressable” in that its location and the identity of theimmobilized probe at that location are known or determinable.

The solid supports can also include a semi-solid support such as acompressible matrix with both a solid and a liquid component, whereinthe liquid occupies pores, spaces or other interstices between the solidmatrix elements. Preferably, the semi-solid support materials includepolyacrylamide, cellulose, poly dimethyl siloxane, polyamide (nylon) andcross-linked agarose, -dextran and -polyethylene glycol. Solid supportsand semi-solid supports can be used together or independent of eachother.

Supports can also include immobilizing media. Such immobilizing mediathat are of use according to the invention are physically stable andchemically inert under the conditions required for nucleic acid moleculedeposition and amplification. A useful support matrix withstands therapid changes in, and extremes of, temperature required for PCR. Thesupport material permits enzymatic nucleic acid synthesis. If it isunknown whether a given substance will do so, it is tested empiricallyprior to any attempt at production of a set of arrays according to theinvention. According to one embodiment of the present invention, thesupport structure comprises a semi-solid (i.e., gelatinous) lattice ormatrix, wherein the interstices or pores between lattice or matrixelements are filled with an aqueous or other liquid medium; typical pore(or ‘sieve’) sizes are in the range of 100 μm to 5 nm. Larger spacesbetween matrix elements are within tolerance limits, but the potentialfor diffusion of amplified products prior to their immobilization isincreased. The semi-solid support is compressible. The support isprepared such that it is planar, or effectively so, for the purposes ofprinting. For example, an effectively planar support might becylindrical, such that the nucleic acids of the array are distributedover its outer surface in order to contact other supports, which areeither planar or cylindrical, by rolling one over the other. Lastly, asupport material of use according to the invention permits immobilizing(covalent linking) of nucleic acid features of an array to it by meansknown to those skilled in the art. Materials that satisfy theserequirements comprise both organic and inorganic substances, andinclude, but are not limited to, polyacrylamide, cellulose and polyamide(nylon), as well as cross-linked agarose, dextran or polyethyleneglycol.

One embodiment is directed to a thin polyacrylamide gel on a glasssupport, such as a plate, slide or chip. A polyacrylamide sheet of thistype is synthesized as follows. Acrylamide and bis-acrylamide are mixedin a ratio that is designed to yield the degree of crosslinking betweenindividual polymer strands (for example, a ratio of 38:2 is typical ofsequencing gels) that results in the desired pore size when the overallpercentage of the mixture used in the gel is adjusted to give thepolyacrylamide sheet its required tensile properties. Polyacrylamide gelcasting methods are well known in the art (see Sambrook et al., 1989,Molecular Cloning. A Laboratory Manual, 2nd Edition, Cold Spring HarborLaboratory Press, Cold Spring Harbor, N.Y., incorporated herein in itsentirety by reference), and one of skill has no difficulty in makingsuch adjustments.

The gel sheet is cast between two rigid surfaces, at least one of whichis the glass to which it will remain attached after removal of theother. The casting surface that is to be removed after polymerization iscomplete is coated with a lubricant that will not inhibit gelpolymerization; for this purpose, silane is commonly employed. A layerof silane is spread upon the surface under a fume hood and allowed tostand until nearly dry. Excess silane is then removed (wiped or, in thecase of small objects, rinsed extensively) with ethanol. The glasssurface which will remain in association with the gel sheet is treatedwith γ-methacryloxypropyltrimethoxysilane (Cat. No. M6514, Sigma; St.Louis, Mo.), often referred to as ‘crosslink silane’, prior to casting.The glass surface that will contact the gel is triply-coated with thisagent. Each treatment of an area equal to 1200 cm² requires 125 μl ofcrosslink silane in 25 ml of ethanol. Immediately before this solutionis spread over the glass surface, it is combined with a mixture of 750μl water and 75 μl glacial acetic acid and shaken vigorously. Theethanol solvent is allowed to evaporate between coatings (about 5minutes under a fume hood) and, after the last coat has dried, excesscrosslink silane is removed as completely as possible via extensiveethanol washes in order to prevent ‘sandwiching’ of the other supportplate onto the gel. The plates are then assembled and the gel cast asdesired.

The only operative constraint that determines the size of a gel that isof use according to the invention is the physical ability of one ofskill in the art to cast such a gel. The casting of gels of up to onemeter in length is, while cumbersome, a procedure well known to workersskilled in nucleic acid sequencing technology. A larger gel, ifproduced, is also of use according to the invention. An extremely smallgel is cut from a larger whole after polymerization is complete.

Note that at least one procedure for casting a polyacrylamide gel withbioactive substances, such as enzymes, entrapped within its matrix isknown in the art (O'Driscoll, 1976, Methods Enzymol., 44: 169-183,incorporated herein in its entirety by reference). A similar protocol,using photo-crosslinkable polyethylene glycol resins, that permitentrapment of living cells in a gel matrix has also been documented(Nojima and Yamada, 1987, Methods Enzymol., 136: 380-394, incorporatedherein in its entirety by reference). Such methods are of use accordingto the invention. As mentioned below, whole cells are typically castinto agarose for the purpose of delivering intact chromosomal DNA into amatrix suitable for pulsed-field gel electrophoresis or to serve as a“lawn” of host cells that will support bacteriophage growth prior to thelifting of plaques according to the method of Benton and Davis (seeManiatis et al., 1982, Molecular Cloning: A Laboratory Manual, ColdSpring Harbor Laboratory Press, Cold Spring Harbor, N.Y., incorporatedherein in its entirety by reference). In short, electrophoresis-gradeagarose (e.g., Ultrapure; Life Technologies/Gibco-BRL) is dissolved in aphysiological (isotonic) buffer and allowed to equilibrate to atemperature of 50° C. to 52° C. in a tube, bottle or flask. Cells arethen added to the agarose and mixed thoroughly, but rapidly (if in abottle or tube, by capping and inversion, if in a flask, by swirling),before the mixture is decanted or pipetted into a gel tray. Iflow-melting point agarose is used, it may be brought to a much lowertemperature (down to approximately room temperature, depending upon theconcentration of the agarose) prior to the addition of cells. This isdesirable for some cell types; however, if electrophoresis is to followcell lysis prior to covalent attachment of the molecules of theresultant nucleic acid pool to the support, it is performed underrefrigeration, such as in a 4° C. to 10° C. ‘cold’ room.

Oligonucleotides immobilized on microarrays include nucleic acids thatare generated in or from an assay reaction. Typically, theoligonucleotides or polynucleotides on microarrays are single strandedand are covalently attached to the solid phase support, usually by a5′-end or a 3′-end. In certain exemplary embodiments, probes areimmobilized via one or more cleavable linkers. The density ofnon-overlapping regions containing nucleic acids in a microarray istypically greater than 100 per cm², and more typically, greater than1000 per cm². Microarray technology relating to nucleic acid probes isreviewed in the following exemplary references: Schena, Editor,Microarrays: A Practical Approach (IRL Press, Oxford, 2000); Southern,Current Opin. Chem. Biol., 2: 404-410 (1998); Nature GeneticsSupplement, 21:1-60 (1999); and Fodor et al, U.S. Pat. Nos. 5,424,186;5,445,934; and 5,744,305.

Methods of immobilizing oligonucleotides to a support are known in theart (beads: Dressman et al. (2003) Proc. Natl. Acad. Sci. USA 100:8817,Brenner et al. (2000) Nat. Biotech. 18:630, Albretsen et al. (1990)Anal. Biochem. 189:40, and Lang et al. Nucleic Acids Res. (1988)16:10861; nitrocellulose: Ranki et al. (1983) Gene 21:77; cellulose:Goldkorn (1986) Nucleic Acids Res. 14:9171; polystyrene: Ruth et al.(1987) Conference of Therapeutic and Diagnostic Applications ofSynthetic Nucleic Acids, Cambridge U.K.; teflon-acrylamide: Duncan etal. (1988) Anal. Biochem. 169:104; polypropylene: Polsky-Cynkin et al.(1985) Clin. Chem. 31:1438; nylon: Van Ness et al. (1991) Nucleic AcidsRes. 19:3345; agarose: Polsky-Cynkin et al., Clin. Chem. (1985) 31:1438;and sephacryl: Langdale et al. (1985) Gene 36:201; latex: Wolf et al.(1987) Nucleic Acids Res. 15:2911). Supports may be coated withattachment chemistry or polymers, such as amino-silane, NHS-esters,click chemistry, polylysine, etc., to bind a nucleic acid to thesupport.

As used herein, the term “attach” refers to both covalent interactionsand noncovalent interactions. A covalent interaction is a chemicallinkage between two atoms or radicals formed by the sharing of a pair ofelectrons (i.e., a single bond), two pairs of electrons (i.e., a doublebond) or three pairs of electrons (i.e., a triple bond). Covalentinteractions are also known in the art as electron pair interactions orelectron pair bonds. Noncovalent interactions include, but are notlimited to, van der Waals interactions, hydrogen bonds, weak chemicalbonds (i.e., via short-range noncovalent forces), hydrophobicinteractions, ionic bonds and the like. A review of noncovalentinteractions can be found in Alberts et al., in Molecular Biology of theCell, 3d edition, Garland Publishing, 1994.

According to certain aspects, affixing or immobilizing nucleic acidmolecules to the substrate is performed using a covalent linker that isselected from the group that includes oxidized 3-methyl uridine, anacrylyl group and hexaethylene glycol. In addition to the attachment oflinker sequences to the molecules of the pool for use in directionalattachment to the support, a restriction site or regulatory element(such as a promoter element, cap site or translational terminationsignal), is, if desired, joined with the members of the pool. Nucleicacids that have been synthesized on the surface of a support may beremoved, such as by a cleavable linker or linkers known to those ofskill in the art. Linkers can be designed with chemically reactivesegments which are optionally cleavable with agents such as enzymes,light, heat, pH buffers, and redox reagents. Such linkers can beemployed to pre-fabricate an in situ solid-phase inactive reservoir of adifferent solution-phase primer for each discrete feature. Upon linkercleavage, the primer would be released into solution for PCR, perhaps byusing the heat from the thermocycling process as the trigger.

It is also contemplated that affixing of nucleic acid molecules to thesupport is performed via hybridization of the members of the pool tonucleic acid molecules that are covalently bound to the support.

Immobilization of nucleic acid molecules to the support matrix accordingto the invention is accomplished by any of several procedures. Directimmobilizing via the use of 3′-terminal tags bearing chemical groupssuitable for covalent linkage to the support, hybridization ofsingle-stranded molecules of the pool of nucleic acid molecules tooligonucleotide primers already bound to the support, or the spreadingof the nucleic acid molecules on the support accompanied by theintroduction of primers, added either before or after plating, that maybe covalently linked to the support, may be performed. Wherepre-immobilized primers are used, they are designed to capture a broadspectrum of sequence motifs (for example, all possible multimers of agiven chain length, e.g., hexamers), nucleic acids with homology to aspecific sequence or nucleic acids containing variations on a particularsequence motif. Alternatively, the primers encompass a syntheticmolecular feature common to all members of the pool of nucleic acidmolecules, such as a linker sequence.

Two means of crosslinking a nucleic acid molecule to a polyacrylamidegel sheet will be discussed in some detail. The first (provided byKhrapko et al., 1996, U.S. Pat. No. 5,552,270) involves the 3′ cappingof nucleic acid molecules with 3-methyl uridine. Using this method, thenucleic acid molecules of the libraries of the present invention areprepared so as to include this modified base at their 3′ ends. In thecited protocol, an 8% polyacrylamide gel (30:1, acrylamide:bis-acrylamide) sheet 30 μm in thickness is cast and then exposed to 50%hydrazine at room temperature for 1 hour. Such a gel is also of useaccording to the present invention. The matrix is then air dried to theextent that it will absorb a solution containing nucleic acid molecules,as described below. Nucleic acid molecules containing 3-methyl uridineat their 3′ ends are oxidized with 1 mM sodium periodate (NaIO₄) for 10minutes to 1 hour at room temperature, precipitated with 8 to 10 volumesof 2% LiClO₄ in acetone and dissolved in water at a concentration of 10pmol/μl. This concentration is adjusted so that when the nucleic acidmolecules are spread upon the support in a volume that covers itssurface evenly and is efficiently (i.e., completely) absorbed by it, thedensity of nucleic acid molecules of the array falls within the rangediscussed above. The nucleic acid molecules are spread over the gelsurface and the plates are placed in a humidified chamber for 4 hours.They are then dried for 0.5 hour at room temperature and washed in abuffer that is appropriate to their subsequent use. Alternatively, thegels are rinsed in water, re-dried and stored at −20° C. until needed.It is thought that the overall yield of nucleic acid that is bound tothe gel is 80% and that of these molecules, 98% are specifically linkedthrough their oxidized 3′ groups.

A second crosslinking moiety that is of use in attaching nucleic acidmolecules covalently to a polyacrylamide sheet is a 5′ acrylyl group,which is attached to the primers. Oligonucleotide primers bearing such amodified base at their 5′ ends may be used according to the invention.In particular, such oligonucleotides are cast directly into the gel,such that the acrylyl group becomes an integral, covalently bonded partof the polymerizing matrix. The 3′ end of the primer remains unbound, sothat it is free to interact with, and hybridize to, a nucleic acidmolecule of the pool and prime its enzymatic second-strand synthesis.

Alternatively, hexaethylene glycol is used to covalently link nucleicacid molecules to nylon or other support matrices (Adams and Kron, 1994,U.S. Pat. No. 5,641,658). In addition, nucleic acid molecules arecrosslinked to nylon via irradiation with ultraviolet light. While thelength of time for which a support is irradiated as well as the optimaldistance from the ultraviolet source is calibrated with each instrumentused due to variations in wavelength and transmission strength, at leastone irradiation device designed specifically for crosslinking of nucleicacid molecules to hybridization membranes is commercially available(Stratalinker, Stratagene). It should be noted that in the process ofcrosslinking via irradiation, limited nicking of nucleic acid strandsoccurs. The amount of nicking is generally negligible, however, underconditions such as those used in hybridization procedures. In someinstances, however, the method of ultraviolet crosslinking of nucleicacid molecules will be unsuitable due to nicking. Attachment of nucleicacid molecules to the support at positions that are neither 5′- nor3′-terminal also occurs, but it should be noted that the potential forutility of an array so crosslinked is largely uncompromised, as suchcrosslinking does not inhibit hybridization of oligonucleotide primersto the immobilized molecule where it is bonded to the support.

Supports described herein may have one or more optically addressablevirtual electrodes associated therewith such that an anion toroidalvortex can be created at a reaction site on the supports describedherein.

Reagent Delivery Systems

According to certain aspects, reagents and washes are delivered that thereactants are present at a desired location for a desired period of timeto, for example, covalently attached dNTP to an initiator sequence or anexisting nucleotide attached at the desired location. A selectednucleotide reagent liquid is pulsed or flowed or deposited at thereaction site where reaction takes place and then may be optionallyfollowed by delivery of a buffer or wash that does not include thenucleotide. Suitable delivery systems include fluidics systems,microfluidics systems, syringe systems, ink jet systems, pipette systemsand other fluid delivery systems known to those of skill in the art.Various flow cell embodiments or flow channel embodiments ormicrofluidic channel embodiments are envisioned which can deliverseparate reagents or a mixture of reagents or washes using pumps orelectrodes or other methods known to those of skill in the art of movingfluids through channels or microfluidic channels through one or morechannels to a reaction region or vessel where the surface of thesubstrate is positioned so that the reagents can contact the desiredlocation where a nucleotide is to be added.

According to another embodiment, a microfluidic device is provided withone or more reservoirs which include one or more reagents which are thentransferred via microchannels to a reaction zone where the reagents aremixed and the reaction occurs. Such microfluidic devices and the methodsof moving fluid reagents through such microfluidic devices are known tothose of skill in the art.

Immobilized nucleic acid molecules may, if desired, be produced using adevice (e.g., any commercially-available inkjet printer, which may beused in substantially unmodified form) which sprays a focused burst ofreagent-containing solution onto a support (see Castellino (1997) GenomeRes. 7:943-976, incorporated herein in its entirety by reference). Sucha method is currently in practice at Incyte Pharmaceuticals and RosettaBiosystems, Inc., the latter of which employs “minimally modified Epsoninkjet cartridges” (Epson America, Inc.; Torrance, Calif.). The methodof inkjet deposition depends upon the piezoelectric effect, whereby anarrow tube containing a liquid of interest (in this case,oligonucleotide synthesis reagents) is encircled by an adapter. Anelectric charge sent across the adapter causes the adapter to expand ata different rate than the tube, and forces a small drop of liquidreagents from the tube onto a coated slide or other support.

Reagents can be deposited onto a discrete region of the support, suchthat each region forms a feature of the array. The feature is capable ofgenerating an anion toroidal vortex as described herein. The desirednucleic acid sequence can be synthesized drop-by-drop at each position,as is true for other methods known in the art. If the angle ofdispersion of reagents is narrow, it is possible to create an arraycomprising many features. Alternatively, if the spraying device is morebroadly focused, such that it disperses nucleic acid synthesis reagentsin a wider angle, as much as an entire support is covered each time, andan array is produced in which each member has the same sequence (i.e.,the array has only a single feature).

The following examples are set forth as being representative of thepresent disclosure. These examples are not to be construed as limitingthe scope of the present disclosure as these and other equivalentembodiments will be apparent in view of the present disclosure, figuresand accompanying claims.

Examples

Exemplary embodiments of the present disclosure are directed to methodsof enzymatic synthesis of user-defined nucleic acid sequences using TdT.The methods according to the present disclosure contemplate four majorparts: physical and chemical control of nucleic acid polymer exposure toNPU, nucleotide analogue substrates for TdT, conditions for TdTpolymerization, and finally, an example implementation of our inventionsfor TdT-based NPUs to synthesize nucleic acids of a defined informationcontent. These novel methods according to the present disclosure can beused for the synthesis of nucleic acid polymers for information storagein DNA. These novel methods according to the present disclosure furtherprovide improved control of the number and nature of nucleotides thattemplate-independent DNA polymerases, such as TdT, incorporate intonucleic acid polymers and enable user-defined synthesis of nucleic acidsequences useful for biological applications.

Controlled NPU Exposure to Nucleic Acid Polymers

The present disclosure provides that limiting the number of nucleotideadditions by TdT can be achieved by controlling one or a combination ofthe following three elements of the polymerization reaction: theprimer/initiator, the nucleotide substrate, or the polymerase. Previousand ongoing attempts at custom DNA synthesis using TdT focus on theprimer/initiator combined with the nucleotide. Specifically, others havetried using reversible-terminator nucleotide analogs to synthesize DNAof a desired sequence. However, it has been found that TdT does notefficiently work with any of the available reversible terminatornucleotide analogues. Furthermore, using such analogues adds to both thecost and complexity of DNA synthesis while increasing synthesis time.The present disclosure provides novel methods of enzymatic synthesisthat focus on controlling the nucleotide and the polymerase, i.e., theNPU, using various physical and chemical control approaches.

In one approach according to the methods of the present disclosure, thetime the initiator/primer is in physical contact with NPU is controlled.In one embodiment, the method of the disclosure provides an efficientway to establish such a physical method of NPU exposure control throughfluidics. An exemplary embodiment of such a method is shown in FIGS. 1Aand 1B, in which initiator oligonucleotides were immobilized on asurface of a fluidic device (called initiator patch or patch). The patchis then exposed to NPUs which include TdT pre-mixed with only one of thefour possible nucleotide triphosphates (dNTPs). As shown in FIG. 1B, themicrofluidic device flows each NPU over the patch at a given rate, thuslimiting the exposure time of the patch to each NPU to generate anextension of a desired base to a desired count or desired distributionof counts. In certain embodiments, the device also allows control overthe order of NPUs, thereby allowing control over the incorporatedsequence and information content (FIG. 1A). For instance, for thesynthesis of the sequence “GATC,” the patch will be serially exposed tofour NPUs. The NPUs will each includes TdT with dGTP, dATP, dTTP, anddCTP, respectively. The fluidic control exposes the patch to each of theNPUs for the optimal time which ensures addition of that specificnucleotide to the entire patch of initiator oligonucleotides.

In another approach according to the methods of the present disclosure,the amount of time the nucleotide substrates are available to the enzymefor extension of the primer/initiator is controlled. In one embodiment,the enzyme “ATP diphosphohydrolase” (Apyrase), which degrades dNTPs, wasadded to a reaction with TdT (FIG. 2A). This addition results in twocompeting reactions: one is the polymerization of free nucleotides byTdT to a nucleic acid polymer and the other is the degradation of freenucleotides available to TdT by Apyrase. The concentration of Apyrasewas optimized which allowed reproducible addition of nucleotideextensions of set lengths. Once a nucleotide was added to the initiatorby the polymerase and its excess was degraded by apyrase, the nextnucleotide would be added to the mixture (FIG. 2B). For instance, forthe synthesis of the sequence “GATC,” the initiator, TdT, and apyrasewere mixed. Then a small amount of dGTP was added to this mix. After afew seconds, once TdT has extended the initiators and apyrase hasdegraded the excess dGTP, a small amount of dATP would be added to themix. So on, a few seconds later dTTP would be added. dCTP would be addeda few seconds after that. This new control strategy obviated thechallenging requirement for high temporal exposure control presented inthe first physical control approach.

The methods of the present disclosure contemplate additional approachesbeyond these two specific examples that provide similar control overexposure of primer/initiator to the NPU. In some embodiments, theseadditional approaches include: activating inactive nucleotides orinactive TdT enzyme by heat, wavelengths of light, or pH, and using aprotease to remove the TdT enzyme as opposed to removing the dNTPs byapyrase from the reaction after a set amount of time, etc.

Nucleotide Analogue Substrates for TdT

In the general scheme of the presently disclosed methods, thedistribution of extension length by TdT is important to ensure efficientand reliable encoding of information into DNA. It has been found thatthe extension efficiency, rate, and extension length distribution ofeach of the four natural nucleotides (A, C, G, and T) was different. Infact, it has been observed that dCTP shows the most optimal behaviorwhile dATP and dTTP show the poorest behavior with respect to TdT-basedDNA synthesis. Given these observations, several nucleotide analogueswere screened to search for nucleotide analogues with a superiorperformance compared to their natural counterparts in TdT-based DNAsynthesis. The following nucleotide analogues with the NPU formulationwhich included Apyrase were explored.

TABLE 1 Screened nucleotide analogues. dATP analogues dTTP analoguesdGTP analogues 1-Borano-dATP dUTP d7-Deaza-dGTP 1-Thio-dATPAminoallyl-dUTP 1-Borano-dGTP 2-Amino-dATP 5-Br-dUTP 1-Thio-dGTPN6-Methyl-dATP 5-Fluoro-dUTP 7-Deaza-dATP 5-Iodo-dUTP 8-Chloro-dATP5-HydroxyM-dUTP 8-Oxo-dATP 5-Aminoallyl-dUTP 5-Propynyl-dUTP5-Propargylamino-dUTP 5-Bromo-dUTP

It has been found that the following nucleotide analogues displayedequally good or superior efficiency, rate, and/or length distributioncompared to their natural counterparts with TdT (see FIG. 3 fornucleotide structures).

TABLE 2 Improved dATP alternatives. 7-Deaza-7-bromo-dATP 1-Borano-dATP(2′-Deoxyadenosine-5′-O-(1-Boranotriphosphate)) 2-Amino-dATP(Diaminopurine) 7-Deaza-dATP 7-Deaza-7-iodo-dATP

TABLE 3 Improved dTTP alternatives. 5-propynyl-dUTP 5-Bromo-dUTP5-Iodo-dUTP 5-Aminoallyl-dUTP 5-Propargylamino-dUTP

In general, it has been observed that all nucleotide analogues that aremore positively charged than their natural counterparts are far moreefficient substrates of TdT. These analogues include, but are notlimited to, 5-Aminoallyl-dUTP and 5-Propargylamino-dUTP.

Additional nucleotide analogues within the scope of the presentdisclosure include

Biochemical Formulations for Controlled TdT Synthesis

It has been found that the following buffer formula is optimal for TdTpolymerization, allowing efficient addition of all nucleotides by TdT:

10 to 20 mM Tris-Acetate 20 to 50 mM Potassium Acetate 5 to 8 mMMagnesium Acetate 0.5-1.0 mM DTT pH 7.9 in 25° C.

Apyrase is also active in above conditions.

Specifically, it has been found the following buffer to be most optimalfor TdT polymerization:

14 mM Tris-Acetate 35 mM Potassium Acetate 7 mM Magnesium Acetate 0.7 mMDTT pH 7.9 in 25° C. Apparatus Implementation

The present disclosure provides exemplary apparatus, protocol, andimplementation of a method of NPU enzymatic synthesis to generate anucleic acid polymer of a given information content. An embodiment ofthis implementation is illustrated in FIG. 4. Each of the four NPUs is aformulation of TdT, Apyrase, and one of the following nucleotides:7-Deaza-7-bromo-dATP, dCTP, dGTP, and 7-propynyl-dUTP.

A robotic dispensing system (Mantis Robot from the company Formulatrix)which can be programmed to reproducibly move in xyz space and todispense liquids at 100 nanoliter increments was used. Using this robot,100 nanoliters of initiator oligos were deposited on ArrayItSuperAldehyde2 coated slides (Cat. SMA2F) at an optimal concentrationbetween 0.04 micromolar and 5 micromolar, and resuspended in 1×Microspotting solution (ArrayIt). The initiator oligos were designedwith a 5 prime amine modification for immobilization to the glasssurface and with deoxyUridines to enable oligo release by USER(Uracil-Specific Excision Reagent) Enzyme as seen:

5Am12-fS3-ctgac: (SEQ ID NO: 4) /5AmMC12/TTTTTTTTTT/ideoxyU//ideoxyU/CTACACTCTTTCCCTACACGACGCTCTTCCGATCT CTGAC

The slides with the initiator oligos were incubated with 1.4×Microspotting solution (ArrayIt) and 500 millimolar NaCl (3.5 milliliter2× oligo spotting solution, 1 milliliter water, 0.5 milliliter of a 5molar NaCl solution) for 24 hours in a closed environment to preventevaporation. The slides were then dried first at room temperature thenincubated at 60° C. for 1 hour. The slide were then washed once withwater, once with 0.1% SDS+1 millimolar Tris HCl at pH 8.0, and threemore times with water (with vigorous shaking the last time).

To reduce the Schiff bases and unreacted aldehydes, a solution of 0.15 gNaBH₄ in 35 milliliter PBS was prepared. After NaBH₄ was dissolved, 15milliliter 100% ethanol was added to the solution. The slides wereincubated in this solution for 15 minutes with tube cap left open toallow the hydrogen gas to escape. The slides were then washed with watertwice.

To denature DNA, the slides were incubated in 80° C. water for threeminutes and then submerged in ice-cold 100% ethanol for thirty seconds(last sequence to denature the oligos and keep them that way). Theslides were ready to be used for enzymatic synthesis once dried bycentrifugation at 500 g for 3 minutes in a conical tube.

The following cycling procedure is used to synthesize DNA of a giveninformation content:

1. 0.2 microliters of the desire nucleotide resuspended in 25% ethanol(or other solvents that could speed up evaporation while maintaining thenucleotide's solubility) was deposited on the oligo spot and dried atroom temperature (this takes a couple of minutes).2. 0.5-1 microliters of the NPU (formulation below) was deposited oneach oligo spot with the dried nucleotide:

Water: 7.5 microliter

3.5× GreenBuffer: 2 microliter

TdT:Apyrase Stock (1 U:1 mU): 0.5 microliter

Total Volume: 10 microliter

3. Following incubation at room temperature, the spot was washed withroom temperature 0.1% SDS once, water twice, and once dried, was readyfor step 1 of the cycling procedure.

Once the sequence has been synthesized, a DNA adapter was ligated to the3 prime end of the extended oligos. Ligation was carried out on theslides overnight at room temperature by flooding the slide surface withthe following mixture in a sealed container to prevent moisture andoxygen:

10 microliter 10X T4 RNA Ligase Buffer (NEB) 10 microliter 10 millimolarATP 50 microliter 50% PEG 8K 10 microliter 5P-cagtc-rS9-dd (10micromolar) 8 microliter T4 RNA Ligase 12 microliter water 100microliter Total Volume

5P-cagtc-rS9-dd/5phos/CAGTC (SEQ ID NO: 5)AGATCGGAAGAGCACACGTCTGAACTCCAGTCA/3ddC/

This ligation mixture was washed off the slides by 0.1% SDS wash and twowashes with water and subsequently dried by ligation.

Samples can be eluted by depositing 1 microliter of the following USERmix:

42.5 microliter 10 millimolar Tris + 0.001% Tween20 5 microliter UDG (2U/ul) 2.5 microliter EndoVIII (10 U/ul) 50 microliter Total Volume

After incubation at 37° C. for 30 minutes, the samples were transferredto independent tubes and diluted with 50 microliter of a 10 millimolarTris+0.001% Tween20 solution. 5 microliters of each reaction wasquantified in quantitative PCR with the appropriate primers such as:

f-tS3 (SEQ ID NO: 6) CTACACTCTTTCCCTACACGAC f-ttS9 (SEQ ID NO: 7)GTGACTGGAGTTCAGACGTGwhich could then be amplified appropriately for high-throughputsequencing platforms known to a skilled in the art, including but notlimited to Illumina, Pacific Bioscience, or Oxford Nanopore.

An Experimental Protocol Summary for Physical Control Materials andMethods

According to an exemplary protocol of the present disclosure, aninitiator oligonucleotide was first immobilized onto a surface calledthe initiator patch, in this exemplary embodiment by UV crosslinking DNAto glass surface. After tethering the initiator to a solid support, thesurface was treated to neutralize the chemical reactive groups such asaldehydes in this case, and to increase hydrophobicity. A pre-fabricatedcustom PDMS device was subsequently plasma treated in order tocovalently attach it to the glass slide with the initiator patch.

Nitrogen pumps were used to push aqueous slugs, i.e. discrete volumes,containing the enzymatic cocktail, through one channel and oil slugs,i.e. discrete volumes, containing the wash solution, through the otherchannel. The pump rates were adjusted to give roughly 100 micron longslugs of the aqueous phase separated by roughly 1 millimeter long slugsof organic phase. The residence time of each aqueous slug on theinitiator patch was adjusted by altering the pump rates, while keepingthe relative rates of the aqueous channel and oil pumps the same. Thetotal reaction time was the sum of all residence times of each aqueousslug passing over the initiator patch while the pumps are active.

After each desired reaction time, the synthesized DNA on the initiatorpatch can be assessed for the number of nucleotides added. By imaging,the length of nucleotides added can be assessed by the use offluorescent nucleotides or hybridization of fluorescent probes. Thesynthesized DNA on the initiator patch can also be released, in thisexemplary embodiment, enzymatically, by the use of USER (Uracil-SpecificExcision Reagent) enzyme which cleaves the uracils that are near the 5prime distal end of the initial initiator oligonucleotide. The cleavedDNA strands are then collected by flow into a tube. These strands aresubsequently PCR amplified and the number of synthesized nucleotidesevaluated by two methods: electrophoresis on agarose or PAGE gels forcursory bulk analysis and sequenced with next-generation sequencingplatforms such as Illumina, Pacific Bioscience, and/or Oxford Nanoporefor quantitative single-molecule analysis.

Detailed Protocol

1. Glass slides were washed with 1M HCl for 10 minutes with shaking,rinsed twice with ultrapure water, washed with acetone for 5 minuteswhile shaking, and air dried.

2. On the backside of the glass slides, a marker was used to mark theplacement spot for the initiator oligo. Oligo ctgac was diluted to 5 uMin PBS. 3 uL of this oligo solution was placed on the glass slides andincubated at 60° C. until dry.

ctgac (SEQ ID NO: 8) TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT/ideoxyU//ideoxyU/CGACGCTCTTCCGATCTCTGAC

3. Using a UV Stratalinker 2400, the oligo was covalently attached tothe glass by exposure to 100 uJ for 6.5 seconds. The slides were thenwashed with 0.1×SSC with 0.2% SDS for 5 minutes with shaking, rinsedonce with water and dried at 60° C. for 10 min.

4. A PDMS mask with, previously casted to contain a 100 micron channelwith a standard T junction (illustration in FIG. 5) was treated withOxygen Plasma at 200 milliwatts for 30 seconds and sealed onto the glassslides such that the oligo patch would be under the part of the channelthat was intended for the initiator.

5. The organic phase was a 7 to 3 mixture of Hexadecane and AR-20Silicon Oil (both obtained from Sigma). An air pump was used tocontinuously pump this organic/wash solution in the device through theOrganic/Wash Input with a back pressure of 10 Mega Pascals.

6. The aqueous reagent was prepared with the following composition:

15 mM Tris-Acetate, 35 mM Potassium Acetate, 7 mM Magnesium Acetate, 1U/uL TdT enzyme, 0.01% Triton X-100, 1 mM Cy5-dATP, pH=8.0.

Another airpump was used to continuously pump this aqueous reagentsolution through the Aqueous/Reagent Input on the device.

7. As a result, roughly 100 micron long slugs of the aqueous phaseseparated by roughly 1 millimeter long slugs of organic phase wereconstantly generated. The total residence time of these aqueous slugs onthe initiator patch could be increased or decreased by respectivelyincreasing or decreasing the total pump-generated pressure in thesystem. The number of slugs that came in contact with the initiatorpatch could be controlled by the total time that the pumps were on.

8. At the end of the experiment the channel was washed with 2×SSC.

9. The amount of polymerization on the initiator patch was assessed byimaging the initiator patch of the device in Cy5 channel using aninverted fluorescence microscope.

The results of this experiment showed that the average number ofnucleotides added to the initiator by each slug, as measured by totalfluorescence intensity, can be controlled by changing the exposure timeof the initiator patch to each slug.

An Experimental Protocol Summary for Chemical Control Materials andMethods

According to an exemplary protocol of the present disclosure, aninitiator oligonucleotide was first immobilized onto a surface, forexample with the use of a 5 prime modified oligonucleotide onto aldehydefunctionalized glass slides. After tethering the initiator to a solidsupport, the surface was treated to neutralize the chemical reactivegroups such as aldehydes in this case, and to increase hydrophobicity.

Dilutions of nucleotides in solvents such as water or ethanol of thefollowing concentration and types were prepared:

0, 15.625, 31.25, 62.5, 125, 250, 500, and 1000 uM dilutions of7-deaza-7-bromo-dATP, 7-propynyl-dUTP, dCTP, and dGTP.

Each of these nucleotides were printed on an oligo spot with a liquidhandling robot followed by printing of the enzymatic mix comprising TdT(Terminal deoxynucleotidyl transferase) and Apyrase. After a specifiedreaction time between the oligonucleotide, printed nucleotide, and printenzymatic mix, the slides were washed and a terminal oligonucleotide wasligated onto the synthesized DNA to allow for subsequent amplification.

Each of the synthesized DNA strands were released off the solid-supportsurface, in this exemplary embodiment, enzymatically, by the use of USER(Uracil-Specific Excision Reagent) enzyme which cleaves the uracils thatare near the 5 prime distal end of the initial initiatoroligonucleotide. These strands were subsequently PCR amplified and thenumber of synthesized nucleotides were evaluated by two methods:electrophoresis on agarose or PAGE gels for cursory bulk analysis andsequenced with next-generation sequencing platforms such as Illumina,Pacific Bioscience, and/or Oxford Nanopore for quantitativesingle-molecule analysis.

Detailed Protocol

1. The following oligo was resuspended in 1× Microspotting solution(ArrayIt):

5Am12-ctgac (SEQ ID NO: 4) /5AmMC12/TTTTTTTTTT/ideoxyU//ideoxyU/CTACACTCTTTCCCTACACGACGCTCTTCCGATCT CTGAC

2. One aldehyde coated slide was spotted with the above oligo mix. Theslide was then incubated at 60° C. for 1 hour.

3. The slide was then washed once with water, once with 0.1% SDS+1 mMTrisHCl, and three more times in with water.

4. To reduce the Schiff bases and unreacted aldehydes, a solution of0.15 g NaBH₄ in 35 mL PBS was prepared. After NaBH₄ was dissolved, 15 mL100% was added to the solution. The slide was incubated in this solutionfor 15 minutes.

5. To denature DNA, the slide was incubated in ˜80° C. water for threeminutes and then submerged in ice-cold 100% ethanol for thirty seconds(last sequence to denature the oligos and keep them that way).

6. Slide was dried by centrifugation at 500 g for 3 minutes.

7. 0, 15.625, 31.25, 62.5, 125, 250, 500, and 1000 uM dilutions of7-deaza-7-bromo-dATP, 7-propynyl-dUTP, dCTP, and dGTP in 25% ethanolwere prepared.

8. A 2 μl droplet of each nucleotide concentration was printed on anoligo spot with a liquid handling robot and then dried at roomtemperature (RT) for a few minutes.

9. A 5 μl droplet of this enzymatic mix was deposited on each spot withdried nucleotide:

15 mM Tris-Acetate, 35 mM Potassium Acetate, 7 mM Magnesium Acetate, 1U/μL TdT enzyme, 0.001 U/μL Apyrase enzyme, pH=8.0.

10. After 4 minutes of incubation at room temperature, the slide waswashed with room temperature 0.1% SDS once and water twice, and thendried again with centrifugation.

11. Ligation was carried out on the slide overnight at room temperaturewith the following mix:

50 mM Tris-HCl, 10 mM MgCl₂, 1 mM DTT, 1 mM ATP, 25% PEG 8K, 1 μM5P-cagtc oligo, 0.8 U/μl T4 RNA ligase 1, pH=7.5

where the oligo 5P-cagtc has the following sequence:

/5phos/CAGTC (SEQ ID NO: 5) AGATCGGAAGAGCACACGTCTGAACTCCAGTCA

12. Ligation mix was washed by 0.1% SDS wash and two washes with water.The slide was dried by centrifugation.

13. Samples were eluted once using 1.0 ul USER mix at 37 C for 30minutes:

10 mM Tris-HCl pH=8, 0.2 U/μL UDG enzyme, 0.5 U/μL Endonuclease VIIIenzyme

14. 2 μL of each template was amplified in a reaction with S1 and S2 asprimers.

S1 (SEQ ID NO: 6) CTACACTCTTTCCCTACACGAC S2 (SEQ ID NO: 7)GTGACTGGAGTTCAGACGTG

15. 5 μL of each PCR product was run on a 4% Agarose gel (as shown inFIG. 6).

These results illustrated that Apyrase effectively limited the averageamount of extension by TdT in each reaction. Furthermore, the amount ofnucleotide used in the reaction can be used to adjust the amount ofthese extensions.

16. 0.5 μl of the PCR product was used in a second PCR with NEBNext DualIndexing Primer Set and sequenced on an Illumina MiSeq with 100 bpsingle read.

Based on analysis of Illumina MiSeq reads, the number of nucleotidesadded to the oligonucleotide initiator were quantified for eachnucleotide type and concentration in addition to the number ofoligonucleotide initiators that received nonzero addition of nucleotidesfor each nucleotide type and concentration (See, FIG. 7 and FIG. 8),where 0 to 7 for each base (i.e. AO to A7) corresponds to increasingconcentrations of a given nucleotide.

Modulating the TdT Enzymatic Activity by pH

The objective of these experiments is to determine the range of pH inwhich TdT is active.

1. A buffer of 50 mM Tris (base) and 50 mM Boric acid was prepared andits pH (initially at ˜8.5) was adjusted to 6.05, 6.9, 7.93, 8.96, 10.02,and 11.07 using acetic acid and sodium hydroxide. These buffers serve as2× buffers in the experiments.

2. Extension reactions were assembled as follows:

Water:

2× Buffer: 10 μl

25 μM initiator: 1 μl

100 mM MgSO₄ or water: 2 μl

1 mM dCTP:

TdT (20 U/μl):

Total Volume: 20 μl

3. Each reaction was incubated for 15 minutes and then loaded on aTBE-Urea gel with an unextended initiator for comparison.

As shown in FIG. 13, the results in the TBE-Urea gel established that pHcan be used to regulate the activity of TdT enzyme in a way that isadaptable for pH-based TdT-control for data storage. It also needs to beestablished that the effects of pH on TdT are reversible; that is, theenzyme's activity can be substantially reduced at an unfavorable pH butcan be reverted back to normal activity at favorable pH. The ensuingexperiment was performed to evaluate this question.

In the following experiment, TdT was incubated at a pH for 15 minuteswithout the nucleotide or the initiator, it was then combined with thenucleotide and the initiator in such a way that the final pH of themixture during polymerization would be different from that of theinitial 15 min incubation.

1. A buffer of 50 mM Tris (base) and 50 mM Boric acid was prepared andits pH (initially at ˜8.5) was adjusted to 6.05, 6.9, 7.93, 8.96, 10.02,and 11.07 using acetic acid and sodium hydroxide. These buffers serve as2× buffers in the experiment.

2. Extension reactions were assembled in two parts:

Part 1:

Water: 5 μl

2× Buffer: 5 μl

100 mM MgAc: 2 μl

TdT (20 U/μl): 1 μl

Total Volume: 10 μl

Part 2:

Water: 3 μl

2× Buffer: 5 μl

25 μM initiator: 1 μl

1 mM dCTP: 1 μl

Total Volume: 10 μl

Eight different extension reactions were assembled with following pHused for the buffer in part1 and part2:

Reaction A B C D E* F G H I Part 1 6  6  6 8 6 + 11 9 11 11 11 BufferPart 2 6 10 11 8 6 + 11 9  6  7 11 Buffer

3. Both parts of each reaction were incubated for 15 minutes, they werethen mixed to form the 20 μl total, then loaded on a TBE-Urea gel:

As shown in FIG. 14, TdT is highly active in pH ranges that are above 6and below 11, and it is substantially inactivated at pH ranges that arebelow 6 and above 11. It was clear from this experiment that theenzymatic activity of TdT could be reversibly inhibited by bothincreasing and reducing the pH. Inhibition of TdT enzymatic activity wasmore effective at pH-11 than it was at pH-6.

For example, as shown in FIG. 14 in lanes A and I, the starting pH was 6and 11 respectively where the enzyme showed little to no polymerizationactivity. Lanes B and C showed that when the enzyme was kept at pH=6 itcould be activated by increasing the pH to more alkaline values. Lanes Gand H showed that when the enzyme was kept at pH=11, it could beactivated by decreasing the pH to more acidic values. Since the enzymeapparently did not denature irreversibly at either pH=6 or pH=11, it wasclear that the effect of pH on the enzymatic activity was reversible andthe enzyme could be activated and inactivated multiple times by changingthe pH. Therefore, it has been demonstrated that TdT could be reversiblyinactivated by changing the pH of the reaction solution to 11 or above.Specifically, the enzyme was highly active in pH from 6 to 10 andlargely inactive at pH greater than 11 but could be reactivated once thepH is lowered back within 6-10 range.

The following modified nucleotide analogues were tested with aninitiator oligonucleotide: 5-Hydroxy-dCTP (hdCTP), 5-Hydroxymethyl-dCTP(hmdCTP), 5-Bromo-dCTP (BrdCTP), 5-Iodo-dCTP (IdCTP) and 5-methyl-dCTP(5m-dCTP). Nucleotides and their respective final concentrations to beused are hdCTP: 0, 2, 4, 8, 16, 32 uM; hmdCTP: 0, 2, 4, 8, 16, 32 uM;BrdCTP: 0, 2, 4, 8, 16, 32 uM; IdCTP: 0, 2, 4, 8, 16, 32 uM; and 5mdCTP:0, 2, 4, 8, 16, 32 uM. The reaction stop solution, STOP&LOAD, wasprepared as 20 ul Novex 2×TBE-Urea loading buffer containing 20 mM EDTA.For each reaction, a 16 ul reaction solution was prepared as follows asa mastermix: 3 μl Water; 10 μl 2× Reaction Buffer; 2 μl 1 uM Primer; 1μl TdT enzymatic mix; for a total volume of 16 ul. Each reaction wasthen mixed with the following components in the specified order: dNTP(various 4× concentrations) at 4.0 μl. All reactions were carried out at22° C. For each reaction, 16 ul of the reaction mix was mixed with 4.0ul of dNTP. After 5 minutes of incubation, 20 ul of STOP&LOAD was mixedwith the reaction. All samples were incubated at 75° C. for 5 minutesand cooled down on ice. 9 ul of each loading mix was loaded on a 15%TBE-Urea gel. Gel was run in 1×TBE at 180V for 90 minutes. Afterrunning, the gel was stained in 1× SybrGold in 1×TBE for 15 minutes,rinsed once with 1×TBE, and imaged on the GelDoc with 5 second exposurein the SybrGold channel. FIG. 15 is a gel image showing results for5BR-dCTP and 5I-dCTP. FIG. 16 is a gel image showing results for 5h-dCTPand 5hm-dCTP. FIG. 17 is a gel image showing results for 5m-dCTP anddCTP.

Other Embodiments

Other embodiments will be evident to those of skill in the art. Itshould be understood that the foregoing description is provided forclarity only and is merely exemplary. The spirit and scope of thepresent invention are not limited to the above examples, but areencompassed by the following claims. All publications and patentapplications cited above are incorporated by reference in their entiretyfor all purposes to the same extent as if each individual publication orpatent application were specifically and individually indicated to be soincorporated by reference.

1. A method for making a polynucleotide comprising (a) delivering areaction reagent mobile phase including at least an error prone templateindependent DNA polymerase, a selected nucleotide triphosphate andcations along a fluidic channel to a reaction site, wherein the reactionsite includes an initiator attached thereto and having a 3′ terminalnucleotide, wherein reaction reagents are present in the reactionreagent mobile phase at selected concentrations, wherein the reactionreagent mobile phase has a selected volume and a selected flow rate toachieve a selected residence time at the reaction site under conditionswhich covalently add one or more of the selected nucleotide to the 3′terminal nucleotide such that the selected nucleotide becomes a 3′terminal nucleotide, (b) delivering an organic wash mobile phase to thereaction site at a fluid flow rate to remove the reaction reagents fromthe reaction site, and (c) repeating steps (a) and (b) until thepolynucleotide is formed, with the proviso that step (b) is not requiredto be performed after the polynucleotide is formed.
 2. The method ofclaim 1 wherein the selected volume and selected flow rate for thereaction reagent mobile phase is determined based on reactivity of theselected nucleotide triphosphate present in the reaction reagent mobilephase.
 3. The method of claim 1 wherein the selected volume and selectedflow rate for the reaction reagent mobile phase differ based on theselected nucleotide triphosphate present in the reaction reagent mobilephase.
 4. The method of claim 1 wherein the selected flow rate for thereaction reagent mobile phase is constant and the selected volumediffers based on the selected nucleotide triphosphate present in thereaction reagent mobile phase.
 5. The method of claim 1 wherein theselected volume of the reaction reagent mobile phase is constant and theselected flow rate differs based on the selected nucleotide triphosphatepresent in the reaction reagent mobile phase.
 6. The method of claim 1wherein the selected flow rate for the reaction reagent mobile phase isconstant and the selected volume differs based on the selectednucleotide triphosphate present in the reaction reagent mobile phase andthe desired number of the selected nucleotides to be added to the 3′ endof the polynucleotide.
 7. The method of claim 1 wherein the selectedvolume of the reaction reagent mobile phase is constant and the selectedflow rate differs based on the selected nucleotide triphosphate presentin the reaction reagent mobile phase and the desired number of theselected nucleotides to be added to the 3′ end of the polynucleotide. 8.The method of claim 1 wherein the reaction site is a surface area on thesurface of the fluidic channel.
 9. The method of claim 1 wherein theselected concentration of reaction reagents in the reaction reagentmobile phase is determined by the selected nucleotide triphosphatepresent in the reaction reagent mobile phase.
 10. The method of claim 1wherein the reaction site is within the fluidic channel.
 11. The methodof claim 1 wherein the reaction site is a structure within the fluidicchannel.
 12. The method of claim 1 wherein the reaction site is acollection of beads within the fluidic channel.
 13. The method of claim1 wherein the reaction site is an electrode on the surface of thefluidic channel.
 14. The method of claim 1 wherein the reaction site isan electrode within the fluidic channel.
 15. The method of claim 1wherein the initiator includes one or more nucleotides.
 16. The methodof claim 1 wherein the residence time is sufficient to limit the numberof covalent additions of the selected nucleotide.
 17. The method ofclaim 1 wherein the organic wash mobile phase is immiscible with thereaction reagent mobile phase.
 18. The method of claim 1 wherein thereaction reagent mobile phase is bounded on either end by an organicwash mobile phase.
 19. The method of claim 1 wherein the organic washmobile phase inactivates the reaction reagent mobile phase at thereaction site.
 20. The method of claim 1 wherein an air plug is usedinstead of or in addition to the organic wash mobile phase.
 21. Themethod of claim 1 wherein an aqueous wash mobile phase is used insteadof or in addition to the organic wash mobile phase.
 22. The method ofclaim 20 wherein an aqueous wash mobile phase is used instead of or inaddition to an air plug.
 23. The method of claim 1 wherein a pluralityof reaction reagent mobile phases bounded on either end by an organicwash mobile phase flow to the reaction site.
 24. The method of claim 1further including the step of monitoring covalent addition of theselected nucleotide.
 25. The method of claim 1 wherein the error pronetemplate independent DNA polymerase is terminal deoxynucleotidetransferase.
 26. The method of claim 1 wherein the cations are one ormore of Zn⁺², Co⁺², Mg⁺² or Mn⁺².
 27. The method of claim 1 wherein theselected nucleotide is a natural nucleotide or a nucleotide analog. 28.The method of claim 1 wherein the selected nucleotide is a memberselected from the group consisting of 1-borano-dATP, 2-amino-dATP,7-deaza-7-bromo-dATP, 7-deaza-7-iodo-dATP, 7-deaza-dATP,5-aminoallyl-dUTP, 5-bromo-dUTP, 5-iodo-dUTP, 5-propargylamino-dUTP,5-propynyl-dUTP, 5-hydroxy-dCTP, 5-hydroxymethyl-dCTP, 5-bromo-dCTP,5-iodo-dCTP and 5-methyl-sCTP.
 29. The method of claim 1 wherein thereaction reagent mobile phase includes a buffer comprising a monovalentsalt, a divalent salt, a buffering agent, and a reducing agent at asuitable pH and temperature.
 30. The method of claim 1 wherein thereaction reagent mobile phase includes a buffer comprising 10 to 20 mMtris-acetate, 20 to 50 mM potassium acetate, 5 to 8 mM magnesiumacetate, 0.5 to 1.0 mM DTT and with a pH of about 2 to 12 and at atemperature of about 10 and 80° C.
 31. The method of claim 1 wherein thereaction reagent mobile phase includes a buffer comprising 14 mMtris-acetate, 35 mM potassium acetate, 7 mM magnesium acetate, 0.7 mMDTT and with a pH of about 7.9 and at a temperature of about 25° C. 32.The method of claim 1 wherein the initiator is attached by a cleavablemoiety.
 33. The method of claim 1 further comprising releasing thepolynucleotide from the reaction site after the desired sequence ofnucleotides has been added to the 3′ end of the polynucleotide.
 34. Themethod of claim 1 further comprising releasing the polynucleotide fromthe reaction site using an enzyme, a chemical, light, heat or othersuitable method or reagent.
 35. The method of claim 1 further comprisingreleasing the polynucleotide from the reaction site, collecting thepolynucleotide, amplifying the polynucleotide and sequencing thepolynucleotide.
 36. A method for making a polynucleotide comprising (a)combining a selected nucleotide triphosphate, cations, an error prone ortemplate independent DNA polymerase, and a nucleotide triphosphateinactivating enzyme at a reaction site including an initiator sequenceattached thereto and having a 3′ terminal nucleotide, wherein reactionreagents are present at selected concentrations and under conditionswhich covalently add one or more of the selected nucleotide to the 3′terminal nucleotide such that the selected nucleotide becomes a 3′terminal nucleotide and under conditions which inactivate freenucleotide triphosphates until free nucleotide triphosphates aresubstantially inactivated, wherein a desired number of the selectednucleotide is added to the initiator sequence, and (b) repeating step(a) until the polynucleotide is formed.
 37. The method of claim 36wherein the nucleotide inactivating enzyme is a nucleotide triphosphatedegrading enzyme.
 38. The method of claim 36 wherein the nucleotidetriphosphate inactivating enzyme is a nucleotide triphosphate degradingenzyme that degrades nucleotide triphosphates at a rate slower than rateof addition of nucleotides by the error prone or template independentDNA polymerase.
 39. The method of claim 36 wherein the nucleotidetriphosphate inactivating enzyme is a nucleotide triphosphate degradingenzyme present at a concentration that degrades nucleotide triphosphatesat a rate slower than rate of addition of nucleotides by the presentconcentration of the error prone or template independent DNA polymerase.40. The method of claim 36 wherein the nucleotide triphosphateinactivating enzyme comprises ATP diphosphohydrolase, dNTPpyrophosphatases, dNTPases, and phosphatases.
 41. The method of claim 36wherein the concentration of nucleotide triphosphate inactivating enzymeis modulated to control addition of one or more nucleotides.
 42. Themethod of claim 36 wherein the nucleotide triphosphate inactivatingenzyme renders free nucleotide triphosphates inactive.
 43. The method ofclaim 36 wherein the nucleotide inactivating enzyme renders freenucleotide triphosphates inactive by degradation.
 44. The method ofclaim 36 wherein the nucleotide inactivating enzyme renders freenucleotide triphosphates inactive by polymerizing them with each other.45. The method of claim 36 wherein the reaction conditions present acompeting reaction between addition of free nucleotide triphosphates tothe initiator sequence and degradation of free nucleotide triphosphates.46. The method of claim 36 wherein the selected nucleotide is added tothe reaction site including the initiator sequence having the terminalnucleotide, the error prone or template independent DNA polymerase andthe nucleotide inactivating enzyme.
 47. The method of claim 36 whereinthe error prone or template independent DNA polymerase and thenucleotide inactivating enzyme are added to the reaction site includingthe initiator sequence having the terminal nucleotide, and the selectednucleotide.
 48. The method of claim 36 wherein the nucleotideinactivating enzyme is added to the reaction site including theinitiator sequence having the terminal nucleotide, the error prone ortemplate independent DNA polymerase and the selected nucleotide underconditions where the polymerase is inactive, and wherein the polymeraseis activated upon addition of the nucleotide inactivating enzyme. 49.The method of claim 36 wherein step (b) is repeated a plurality of timesafter which the reaction reagents are removed from the reaction site andadditional reaction reagents are provided to the reaction site.
 50. Themethod of claim 47 wherein the reaction reagents are removed from thereaction site and additional reaction reagents are provided to thereaction site after each round of addition.
 51. The method of claim 48wherein the reaction reagents are removed from the reaction site andadditional reaction reagents are provided to the reaction site aftereach round of addition.
 52. A method for making a polynucleotidecomprising (a) combining a selected inactive nucleotide, cations, anerror prone or template independent DNA polymerase at a reaction siteincluding an initiator sequence attached thereto and having a 3′terminal nucleotide, activating the selected inactive nucleotide,wherein reaction reagents are present at selected concentrations andunder conditions which covalently add one or more of a selectedactivated nucleotide to the 3′ terminal nucleotide such that theselected activated nucleotide becomes a 3′ terminal nucleotide and underconditions wherein a desired number of the selected activated nucleotideis added to the initiator sequence, and (b) repeating step (a) until thepolynucleotide is formed.
 53. The method of claim 52 wherein theinactive nucleotide is rendered active by a chemical reaction, anenzyme, heat, light or pH.
 54. The method of claim 52 wherein theinactive nucleotide includes a protecting group and the protecting groupis removed.
 55. The method of claim 54 wherein the inactive nucleotidecomprises NPE-caged nucleotides or similar caged nucleotides that areremoved by light, heat, an enzyme, a chemical reaction, or pH.
 56. Themethod of claim 55 wherein the NPE-caged nucleotides comprisedeoxynucleotide 5′-Triphosphate, P3-(1-(2-Nitrophenyl)Ethyl) esters. 57.The method of claim 52 wherein the selected inactive nucleotide in anucleoside, nucleotide monophosphate, or nucleotide diphosphate formthat is rendered into the active nucleotide triphosphate form by anactivating enzyme such as nucleotide diphosphate kinase.
 58. The methodof claim 52 wherein the inactive nucleotide is rendered active at a ratewhich allows addition of one or more activated nucleotides.
 59. Themethod of claim 52 wherein the inactive nucleotide is rendered active ata rate which allows addition of one or more activated nucleotides afterwhich either the activated nucleotides or the polymerase is renderedinactive.
 60. The method of claim 52 wherein the inactive nucleotide isrendered active allowing addition of one or more activated nucleotidesafter which the polymerase is rendered inactive.
 61. The method of claim52 wherein the polymerase is rendered inactive by a chemical reaction,divalent cations, an enzyme, heat, light or pH.
 62. The method of claim52 wherein the selected inactive nucleotide is added to the reactionsite including the initiator sequence having the terminal nucleotide,and the error prone or template independent DNA polymerase and theinactive nucleotide is activated.
 63. The method of claim 52 whereinstep (b) is repeated a plurality of times after which the reactionreagents are removed from the reaction site and additional reactionreagents are provided to the reaction site.
 64. A method for making apolynucleotide comprising (a) combining a selected nucleotidetriphosphate, cations, an inactive error prone or template independentDNA polymerase at a reaction site including an initiator sequenceattached thereto and having a 3′ terminal nucleotide, activating theinactive error prone or template independent DNA polymerase, whereinreaction reagents are present at selected concentrations and underconditions which covalently add one or more of a selected nucleotide tothe 3′ terminal nucleotide such that the selected nucleotide becomes a3′ terminal nucleotide and under conditions wherein a desired number ofthe selected nucleotide is added to the initiator sequence, and (b)repeating step (a) until the polynucleotide is formed.
 65. The method ofclaim 64 wherein the inactive error prone or template independent DNApolymerase is rendered active by a chemical reaction, divalent cations,an enzyme, heat, light or pH.
 66. The method of claim 64 wherein theinactive error prone or template independent DNA polymerase is renderedactive by a chemical reaction, an enzyme, heat, light or pH and renderedinactive again by a chemical reaction, an enzyme, heat, light or pHafter addition of the desired number of the selected nucleotide onto theinitiator.
 67. The method of claim 64 wherein the inactive error proneor template independent DNA polymerase includes a protecting group andthe protecting group is removed.
 68. The method of claim 67 wherein theprotecting group comprises a chemical group that is incorporated intothe polymerase and is removable by light, heat, pH, or enzymes tocontrol the polymerase activity.
 69. The method of claim 64 wherein theinactive error prone or template independent DNA polymerase is renderedactive at a rate which allows addition of one or more nucleotides. 70.The method of claim 64 wherein the inactive error prone or templateindependent DNA polymerase is rendered active at a rate which allowsaddition of one or more nucleotides after which either the nucleotidesor the polymerase is rendered inactive.
 71. The method of claim 64wherein the inactive error prone or template independent DNA polymeraseis rendered active allowing addition of one or more nucleotides afterwhich the polymerase is rendered inactive.
 72. The method of claim 64wherein the polymerase is rendered inactive by a chemical reaction, anenzyme, heat, light or pH.
 73. The method of claim 64 wherein theinactive error prone or template independent DNA polymerase is added tothe reaction site including the initiator sequence having the terminalnucleotide, and the selected nucleotide triphosphate and wherein theinactive error prone or template independent DNA polymerase isactivated.
 74. The method of claim 64 wherein step (b) is repeated aplurality of times after which the reaction reagents are removed fromthe reaction site and additional reaction reagents are provided to thereaction site.
 75. A method for making a polynucleotide comprising (a)combining a selected nucleotide triphosphate, cations, an error prone ortemplate independent DNA polymerase at a reaction site including aninitiator sequence attached thereto and having a 3′ terminal nucleotide,wherein reaction reagents are present at selected concentrations andunder conditions which covalently add one or more of a selectednucleotide to the 3′ terminal nucleotide such that the selectednucleotide becomes a 3′ terminal nucleotide and wherein the error proneor template independent DNA polymerase is inactivated to terminateaddition of the selected nucleotide, and (b) repeating step (a) untilthe polynucleotide is formed.
 76. The method of claim 75 wherein theinactive error prone or template independent DNA polymerase is renderedactive by a chemical reaction, an enzyme, heat, light or pH.
 77. Themethod of claim 75 wherein the active error prone or templateindependent DNA polymerase is rendered inactive by a chemical reaction,an enzyme, heat, light or pH after the addition of a desired number ofthe selected nucleotide and rendered active again by a chemicalreaction, an enzyme, heat, light or pH for the addition of the nextselected nucleotide to the 3′ terminal nucleotide of the polynucleotide.78. The method of claim 75 wherein the inactive error prone or templateindependent DNA polymerase includes a protecting group and theprotecting group is removed.
 79. The method of claim 78 wherein theprotecting group comprises a chemical group that is incorporated intothe polymerase and is removable by light, heat, pH, or enzymes tocontrol the polymerase activity.
 80. The method of claim 75 wherein theerror prone or template independent DNA polymerase is rendered inactiveat a rate which allows addition of one or more nucleotides.
 81. Themethod of claim 75 wherein the error prone or template independent DNApolymerase is rendered inactive at a rate which allows addition of oneor more nucleotides.
 82. The method of claim 75 wherein the error proneor template independent DNA polymerase is added to the reaction siteincluding the initiator sequence having the terminal nucleotide, and theselected nucleotide triphosphate and wherein the error prone or templateindependent DNA polymerase is rendered inactive.
 83. The method of claim75 wherein step (b) is repeated a plurality of times after which thereaction reagents are removed from the reaction site and additionalreaction reagents are provided to the reaction site.
 84. A method formaking a polynucleotide comprising (a) combining a selected inactivenucleotide, cations, an inactive error prone or template independent DNApolymerase at a reaction site including an initiator sequence attachedthereto and having a 3′ terminal nucleotide, activating the nucleotideand activating the error prone or template independent DNA polymerase,wherein reaction reagents are present at selected concentrations andunder conditions which covalently add one or more of a selectednucleotide to the 3′ terminal nucleotide such that the selectednucleotide becomes a 3′ terminal nucleotide, and (b) repeating step (a)until the polynucleotide is formed.
 85. The method of claim 84 whereineither the active nucleotide or the active error prone or templateindependent DNA polymerase is rendered inactive to terminate addition ofthe selected nucleotide.
 86. The method of claim 84 wherein the activeerror prone or template independent DNA polymerase is rendered inactiveby a chemical reaction, an enzyme, heat, light or pH after the additionof a desired number of the selected nucleotide and rendered active againby a chemical reaction, an enzyme, heat, light or pH for the addition ofthe next selected nucleotide to the 3′ terminal nucleotide of thepolynucleotide.
 87. The method of claim 84 wherein the inactive errorprone or template independent DNA polymerase is rendered active by achemical reaction, an enzyme, heat, light or pH.
 88. The method of claim84 wherein the inactive error prone or template independent DNApolymerase includes a protecting group and the protecting group isremoved.
 89. The method of claim 88 wherein the protecting groupcomprises a chemical group that is incorporated into the polymerase andis removable by light, heat, pH, or enzymes to control the polymeraseactivity.
 90. The method of claim 84 wherein the inactive nucleotide isrendered active by a chemical reaction, an enzyme, heat, light or pH.91. The method of claim 90 wherein the inactive nucleotide includes aprotecting group and the protecting group is removed.
 92. The method ofclaim 91 wherein the inactive nucleotide comprises NPE-caged nucleotidesor similar caged nucleotides that are removed by light, heat, an enzyme,a chemical reaction, or pH.
 93. The method of claim 92 wherein theNPE-caged nucleotides comprise deoxynucleotide 5′-Triphosphate,P3-(1-(2-Nitrophenyl)Ethyl) esters.
 94. The method of claim 84 whereinthe selected inactive nucleotide in a nucleoside, nucleotidemonophosphate, or nucleotide diphosphate form that is rendered into theactive nucleotide triphosphate form by an activating enzyme such asnucleotide diphosphate kinase.
 95. The method of claim 84 wherein eitherthe inactive nucleotide or inactive error prone or template independentDNA polymerase is rendered active at a rate which allows addition of oneor more nucleotides.
 96. The method of claim 84 wherein step (b) isrepeated a plurality of times after which the reaction reagents areremoved from the reaction site and additional reaction reagents areprovided to the reaction site.